Viral vectors encoding recombinant fix with increased expression for gene therapy of hemophilia b

ABSTRACT

The present disclosure provides, among other aspects, codon-altered polynucleotides encoding Factor IX variants for expression in mammalian cells. In some embodiments, the disclosure also provides mammalian gene therapy vectors and methods for treating hemophilia B.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.62/509,616, filed on May 22, 2017, which is herein expresslyincorporated by reference in its entirety for all purposes.

REFERENCE TO A “SEQUENCE LISTING,” A TABLE, OR A COMPUTER PROGRAM,LISTING APPENDIX SUBMITTED ON A COMPACT DISK

This disclosure incorporates by reference the Sequence Listing text copysubmitted herewith, which was created on May 21, 2018, entitled008073_5117_US_Sequence_Listing.txt which is 73 kilobytes in size.

BACKGROUND OF THE DISCLOSURE

Blood coagulation proceeds through a complex and dynamic biologicalpathway of interdependent biochemical reactions, referred to as thecoagulation cascade. Coagulation Factor VIII (FVIII) and Factor IX (FIX)are key components in the cascade. Factor VIII is recruited to bleedingsites, and forms a Xase complex with activated Factor IX and Factor X(FX). The Xase complex activates FX, which in turn activates prothrombinto thrombin, which then activates other components in the coagulationcascade to generate a stable clot (reviewed in Saenko et al., TrendsCardiovasc. Med., 9:185-192 (1999); Lenting et al., Blood, 92:3983-3996(1998)).

Hemophilia B is a congenital X-linked bleeding disorder characterized bya deficiency in Factor IX activity. Generally, diminished FactorVIII/Factor IX activity inhibits a positive feedback loop in thecoagulation cascade. This causes incomplete coagulation, which manifestsas bleeding episodes with increased duration, extensive bruising,spontaneous oral and nasal bleeding, joint stiffness and chronic pain,and possibly internal bleeding and anemia in severe cases. (Zhang etal., Clinic. Rev. Allerg. Immunol., 37:114-124 (2009)).

Conventionally, hemophilia B is treated by Factor IX replacementtherapy, which consists of administering Factor IX protein (e.g.,plasma-derived or recombinantly-produced Factor IX) to an individualwith hemophilia B. Factor IX is administered prophylactically to preventor reduce frequency of bleeding episodes, in response to an acutebleeding episode, and/or perioperatively to manage bleeding duringsurgery. However, there are several undesirable features of Factor IXreplacement therapy.

First, Factor IX replacement therapy is used to treat or managehemophilia B, but does not cure the underlying Factor IX deficiency.Because of this, individuals with hemophilia B require Factor IXreplacement therapy for the duration of their lives. Continuoustreatment is expensive and requires the individual to maintain strictcompliance, as missing only a few prophylactic doses can have seriousconsequences for individuals with severe hemophilia B.

Second, because conventional Factor IX products have a relatively shorthalf-life in vivo, about 24 hours, prophylactic Factor IX replacementtherapy requires administration two or three times weekly. This places aburden on the individual to maintain compliance throughout their life.While third generation “long-acting” Factor IX drugs may reduce thefrequency of administration, prophylactic Factor FIX replacement therapywith these drugs still requires monthly, weekly, or more frequentadministration in perpetuity. For example, prophylactic treatment withNonacog beta pegol [pegylated recombinant Factor IX] (Novo Nordisk, U.S.and EP regulatory approval pending) still requires weekly administration(Collins P. W., et al., Blood, 124(26):3880-86 (2014)). Moreover, thelong-term effects of chemically modified biologics (e.g., pegylatedpolypeptides) are not yet fully understood.

Third, up to 5% of severe hemophilia B patients Factor IX replacementtherapy form anti-Factor IX inhibitor antibodies, rendering the therapyinefficient (Osooli and Berntorp, J. Intern. Med., 277(1):1-15 (2015)).Unlike Factor VIII bypass therapies that may be used to treat hemophiliaA patients who have developed anti-Factor VIII inhibitory antibodies, noFactor IX bypass therapy exists for the treatment of hemophilia B.

Fourth, Factor IX replacement therapy is expensive, ranging from about$1,000 to about $3,000 per dose, depending on the weight of the patient(Hemophilia Federation of America online materials). Thus, with twiceweekly dosing, Factor IX replacement therapy may cost up to $300,000annually.

Gene therapy holds great promise for the treatment of hemophilia Bbecause it would remedy the underlying under-expression of functionalFactor IX activity (e.g., due to missense or nonsense mutations), ratherthan provide a one-time dose of Factor IX activity to the individual.Because of the difference in the mechanism for providing Factor IX, ascompared to Factor IX replacement therapy, a single administration of aFactor IX gene therapy vector may provide an individual with sufficientlevels of Factor IX for several years, if not longer. This reduces thecost of treatment and eliminates the need for continued patientcompliance.

Proof of concept for Factor IX gene therapy treatment of hemophilia Bhas been shown. See, e.g., Manno C. S., et al., Nat Med., 12(3):342-47(2006). However, questions remain as to whether therapeuticallyeffective amounts of Factor IX can be expressed for sufficient periodsof time. See, e.g., Giangrande, Semin Thromb Hemost. 42(5):513-17(2016).

Several attempts have been made to construct codon-optimized Factor IX.For example, WO 2006/036502 discloses a codon-optimized Factor IX AAVgene therapy vector with an ApoE HCR-1 enhancer and an alpha-1antitrypsin (AAT) promoter. Similarly, WO 2014/064277 and WO 2016/146757disclose codon-optimized Factor VIII and Factor IX AAV gene therapyvectors that include one or more copies of a liver-specific SERPINregulatory element. Finally, WO 2016/210170 discloses codon-optimizedFactor IX AAV gene therapy vectors with an ApoE HCR-1 enhancer and analpha-1 antitrypsin (AAT) promoter.

BRIEF SUMMARY OF DISCLOSURE

Accordingly, there is a need for improved Factor IX gene therapyconstructs. For example, there is a need for synthetic, codon-alterednucleic acids encoding Factor IX that are more efficiently packagedinto, and delivered via, gene therapy vectors. There is also a need forsynthetic, codon-altered nucleic acids that express Factor IX moreefficiently. There is also a need for codon-altered nucleic acidsencoding Factor IX polypeptides with improved folding properties,improved secretion from expressing cells, and/or increased activity, ascompared to wild-type Factor IX. Such Factor IX encoding, codon-alterednucleic acids allow for improved treatment of Factor IX deficiencies(e.g., hemophilia B). The above deficiencies and other problemsassociated with the treatment of Factor IX deficiencies (e.g.,hemophilia B) are reduced or eliminated by the disclosed codon-alterednucleic acids encoding Factor IX proteins.

In one aspect, nucleic acid compositions (e.g., codon-alteredpolynucleotides) encoding Factor IX and Factor IX variants aredescribed. The nucleic acid compositions include polynucleotides withhigh sequence identity to the CS02, CS03, CS04, CS05, and CS06 sequencesencoding Factor IX, as described herein. The nucleic acid compositionsdescribed herein provide increased Factor IX expression relative towild-type Factor IX coding sequences. The nucleic acid compositions alsoallow for increased production of AAV-based gene therapy virions. Insome embodiments, the nucleic acid compositions described herein havedecreased GC content and or include fewer CpG dinucleotides, as comparedto wild-type sequences encoding Factor IX.

In some embodiments, a nucleic acid composition includes apolynucleotide encoding Factor IX that has a nucleotide sequence with atleast 95% sequence identity (e.g., at least 95%, 96%, 97%, 98%, 99%, or100% sequence identity) to a disclosed sequence selected from CS02-FL-NA(SEQ ID NO:5), CS02-MP-NA (SEQ ID NO:13), CS03-FL-NA (SEQ ID NO:6),CS03-MP-NA (SEQ ID NO: 14), CS04-FL-NA (SEQ ID NO:7), CS04-MP-NA (SEQ IDNO: 15), CS05-FL-NA (SEQ ID NO:8), CS05-MP-NA (SEQ ID NO:16), CS06-FL-NA(SEQ ID NO:9), and CS06-MP-NA (SEQ ID NO: 17).

In some embodiments, a nucleic acid composition includes apolynucleotide encoding Factor IX that has a nucleotide sequence with atleast 95% sequence identity (e.g., at least 95%, 96%, 97%, 98%, 99%, or100% sequence identity) to a disclosed sequence encoding a Factor IXlight chain (e.g., CS02-LC-NA (SEQ ID NO:42), CS03-LC-NA (SEQ ID NO:44),CS04-LC-NA (SEQ ID NO:46), CS05-LC-NA (SEQ ID NO:48), or CS06-LC-NA (SEQID NO:50)) and a disclosed sequence encoding a Factor IX heavy chain(e.g., CS02-HC-NA (SEQ ID NO:41), CS03-HC-NA (SEQ ID NO:43), CS04-HC-NA(SEQ ID NO:45), CS05-HC-NA (SEQ ID NO:47), or CS06-HC-NA (SEQ IDNO:49)).

In some embodiments, a nucleic acid composition includes apolynucleotide that encodes a Factor IX polypeptide having a lightchain, a heavy chain, and a polypeptide linker joining the C-terminus ofthe light chain to the N-terminus of the heavy chain (e.g., anactivation peptide). The light chain of the Factor IX polypeptide isencoded by a first nucleotide sequence with high sequence identity toone of CS02-LC-NA (SEQ ID NO:42), CS03-LC-NA (SEQ ID NO:44), CS04-LC-NA(SEQ ID NO:46), CS05-LC-NA (SEQ ID NO:48), and CS06-LC-NA (SEQ IDNO:50). The heavy chain of the Factor IX polypeptide is encoded by asecond nucleotide sequence with high sequence identity to one ofCS02-HC-NA (SEQ ID NO:41), CS03-HC-NA (SEQ ID NO:43), CS04-HC-NA (SEQ IDNO:45), CS05-HC-NA (SEQ ID NO:47), and CS06-HC-NA (SEQ ID NO:49). Thepolypeptide linker comprises a protease cleavage site (e.g., two FactorXIa cleavage sites).

In some embodiments of the polynucleotides described above, thepolypeptide linker has an amino acid sequence with high sequenceidentity to the wild-type Factor IX activation peptide FIX-AP-AA (SEQ IDNO:56; amino acids 192-226 of FIX-FL-AA (SEQ ID NO:2)). In someembodiments, the polypeptide linker is encoded by a third nucleic acidsequence having high sequence identity to one of CS02-AP-NA (SEQ IDNO:57), CS03-AP-NA (SEQ ID NO:58), CS04-AP-NA (SEQ ID NO:59), CS05-AP-NA(SEQ ID NO:60), and CS06-AP-NA (SEQ ID NO:61).

In some embodiments, the codon-altered polynucleotides described hereinencode a pre-pro-Factor IX polypeptide, e.g., where the encoded FactorIX protein includes a signal peptide and a pro-peptide. In someembodiments, the signal peptide, the pro-peptide, or both the signalpeptide and the pro-peptide are encoded by a codon-altered sequence. Insome embodiments, the signal peptide, the pro-peptide, or both thesignal peptide and the pro-peptide are encoded by a wild-type sequence,while the portion of the nucleic acid encoding the mature Factor IXsingle-chain polypeptide (e.g., FIX-MP-AA (SEQ ID NO:10); amino acids47-461 of FIX-FL-AA (SEQ ID NO:2)) is codon altered.

In some embodiment, the codon-altered polynucleotides described hereinencode a Factor IX variant polypeptide, e.g., having one or more aminoacid substitution with respect to the wild-type Factor IX amino acidsequence (e.g., FIX-FL-AA (SEQ ID NO:2) or FIX-MP-AA (SEQ ID NO: 10)).In some embodiments, the Factor IX variant is a hyperactive Factor IXvariant with increased Factor IX activity, as compared to wild-typeFactor IX. In a particular embodiment, the encoded Factor IX polypeptidehas a ‘Padua’ R384L amino acid substitution (relative to the Factor IXpre-pro-polypeptide sequence FIX-FL-AA (SEQ ID NO:2), R338L amino acidsubstitution relative to the mature Factor IX single-chain sequenceFIX-MP-AA (SEQ ID NO: 10)).

In one aspect, methods for treating hemophilia B are described. Themethods include administering to a patient in need thereof a nucleicacid composition (e.g., a codon-altered Factor IX polynucleotideconstruct) described herein (e.g., a polynucleotide having high sequenceidentity to a CS02, CS03, CS04, CS05, or CS06 Factor IX codingsequence). In some embodiments, the Factor IX polynucleotide constructis a mammalian gene therapy vector, as described herein. In a particularembodiment, the Factor IX polynucleotide construct is anadeno-associated virus (AAV) vector. In some embodiments, the genetherapy vector includes one or more copies of a liver-specificregulatory control element (e.g., 1 to 3 copies of a CRM8 regulatorycontrol element).

In one aspect, methods for producing an adeno-associated virus (AAV)particle are described. The method includes introducing a nucleic acidcomposition (e.g., a codon-altered Factor IX polynucleotide construct)described herein (e.g., a polynucleotide having high sequence identityto a CS02, CS03, CS04, CS05, or CS06 Factor IX coding sequence) into amammalian host cell, wherein the polynucleotide is competent forreplication in the mammalian host cell.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1 illustrates exemplary Factor IX gene therapy constructs, inaccordance with some implementations. The sequence elements forself-complementary (A, B) and single-stranded (C, D) vectors are shownwithout (A, C) and with (B, D) liver-specific cis-regulatory modules(CRM8).

FIG. 2 shows the wild-type Factor IX coding sequence (SEQ ID NO: 1) foraccession number CCDS14666.1 (“FIX-FL-NA”).

FIG. 3A and FIG. 3B shows the amino acid sequences of two wild-typeFactor IX pre-pro-polypeptide isoforms expressed in humans. FIG. 3Ashows the wild-type amino acid sequence for the first, longer Factor IXpre-pro-polypeptide isoform (SEQ ID NO:2) corresponding to UniProtaccession number P00740 and NCBI accession number NP_000124.1(“FIX-FL-AA”).

FIG. 3B shows the wild-type amino acid sequence for the second, shorterFactor IX pre-pro-polypeptide isoform (SEQ ID NO:3) corresponding toNCBI accession number NP_001300842.1 (“FIX2-FL-AA”).

FIG. 4 shows the Padua (R384L) Factor IX amino acid sequence (SEQ IDNO:4; “FIXp-FL-AA”).

FIG. 5 shows the CS02 codon-altered nucleotide sequence (SEQ ID NO:5)encoding a Factor IX variant with an R384L amino acid substitution(CS02-FL-NA), in accordance with some implementations.

FIG. 6 shows the CS03 codon-altered nucleotide sequence (SEQ ID NO:6)encoding a Factor IX variant with an R384L amino acid substitution(CS03-FL-NA), in accordance with some implementations.

FIG. 7 shows the CS04 codon-altered nucleotide sequence (SEQ ID NO:7)encoding a Factor IX variant with an R384L amino acid substitution(CS04-FL-NA), in accordance with some implementations.

FIG. 8 shows the CS05 codon-altered nucleotide sequence (SEQ ID NO:8)encoding a Factor IX variant with an R384L amino acid substitution(CS05-FL-NA), in accordance with some implementations.

FIG. 9 shows the CS06 codon-altered nucleotide sequence (SEQ ID NO:9)encoding a Factor IX variant with an R384L amino acid substitution(CS06-FL-NA), in accordance with some implementations.

FIG. 10 illustrates FIX antigen levels in wild-type mice injected with aCS02 gene therapy construct having 0, 1, 2, or 3 copies of a CRM8liver-specific cis-regulatory control element, at a dose of 2×10E11vg/kg body weight.

FIG. 11A and FIG. 11B show the amino acid sequences of two single-chain,wild-type Factor IX protein isoforms (e.g., lacking signal andpropeptides) expressed in humans. FIG. 11A shows the wild-type aminoacid sequence for the first, longer Factor IX pre-pro-polypeptideisoform (SEQ ID NO: 10) corresponding to UniProt accession number P00740and NCBI accession number NP_000124.1 (“FIX-MA-AA”). FIG. 11B shows thewild-type amino acid sequence for the second, shorter Factor IXpre-pro-polypeptide isoform (SEQ ID NO:11) corresponding to NCBIaccession number NP_001300842.1 (“FIX2-MA-AA”).

FIG. 12 shows the single-chain Factor IX(R338L) “Padua” amino acidsequence (SEQ ID NO: 12; “FIXp-MP-AA”).

FIG. 13 shows the CS02 codon-altered nucleotide sequence (SEQ ID NO:13)encoding a single-chain Factor IX variant with an R338L amino acidsubstitution (CS02-MP-NA), in accordance with some implementations.

FIG. 14 shows the CS03 codon-altered nucleotide sequence (SEQ ID NO:14)encoding a single-chain Factor IX variant with an R338L amino acidsubstitution (CS03-MP-NA), in accordance with some implementations.

FIG. 15 shows the CS04 codon-altered nucleotide sequence (SEQ ID NO:15)encoding a single-chain Factor IX variant with an R338L amino acidsubstitution (CS04-MP-NA), in accordance with some implementations.

FIG. 16 shows the CS05 codon-altered nucleotide sequence (SEQ ID NO:16)encoding a single-chain Factor IX variant with an R338L amino acidsubstitution (CS05-MP-NA), in accordance with some implementations.

FIG. 17 shows the CS06 codon-altered nucleotide sequence (SEQ ID NO:17)encoding a single-chain Factor IX variant with an R338L amino acidsubstitution (CS06-MP-NA), in accordance with some implementations.

FIG. 18 shows nucleic acid sequences (NA) encoding the pre-pro-peptide(PPP) of a number of constructs described herein, in accordance withsome implementations.

FIG. 19 shows nucleic acid sequences (NA) encoding the signal peptide(SP) for a number of constructs described herein, in accordance withsome implementations.

FIG. 20 shows nucleic acid sequences (NA) encoding the pro-peptide (PP)for a number of constructs described herein, in accordance with someimplementations.

FIG. 21 shows the amino acid sequence (AA) of the FIX pre-pro-peptide(PPP).

FIG. 22 shows the amino acid sequence (AA) of the FIX signal peptide(SP).

FIG. 23 shows the amino acid sequence (AA) of the FIX pro-peptide (PP).

FIG. 24 shows the nucleic acid sequence of the CRM8 sequence (SEQ IDNO:39).

FIGS. 25A and B shows the nucleic acid sequence of the CS06-CRM8.3-ssVconstruct (SEQ ID NO:40).

DETAILED DESCRIPTION OF DISCLOSURE I. Introduction

AAV-based gene therapy holds great promise for the treatment ofhemophilia. For hemophilia B, first clinical data are encouraging inthat FIX levels of about 10% can be maintained in at least some patientsfor more than 1 year. For example, in initial human trials demonstratedthat hepatic artery catherization of AVV-FIX constructs resulted intransient expression of Factor IX in vivo. Kay M. et al., Nat Genet.24(3):257-61 (2000). However, the transduction resulted in modestactivation of the immune system against AAV-derived capsid antigens.Manno C. S. et al., Nat Med. 12(3):342-47 (2006) and Mingozzi F. et al.,Nat Med. 13(4):419-22 (2007).

Non-viral vectors may be less immunogenic because they are based ondelivery of naked DNA or DNA associated with non-antigenic carriers(e.g., inert polymers, lipids, or nanoparticles). However, cellulartransfection rates of non-viral vectors are lower than those for viraldelivery vectors. Additionally, long-term expression from non-viralvectors is hampered by the presence of bacterial sequences used forlarge-scale production of the constructs.

These challenges, however, cannot be addressed by simply administeringhigher doses of the gene therapy construct. According to currentknowledge, the vector dose of an AAV-based gene therapy vector shouldnot be increased above 2×10¹² vg/kg bodyweight. This is because at suchhigh doses a T cell immune response is triggered, which destroystransduced cells and, as a consequence, transgene expression is reducedor even eliminated. Therefore, strategies to improve the expression ofFIX are needed to make FIX gene therapy a viable therapeutic option forhemophilia B patients.

Thus, improved Factor IX polypeptide constructs that support improvedFactor IX expression and activity would improve both therapeuticapproaches. For example, viral delivery methods would be improved byreducing the initial dose of the construct, thereby reducing stimulationof the subject's immune system. Methods relying on administration ofnaked DNA would be improved by supporting greater Factor IX activitywith fewer copies of the therapeutic polynucleotide.

The present disclosure relates to the discovery of codon-altered FactorIX variant coding sequences that solve these and other problemsassociated with Factor IX gene therapy. For example, the polynucleotidesdisclosed herein provide markedly improved Factor IX expression andactivity in a mammalian host. In some implementations, these advantagesare realized by using Factor IX-encoding polynucleotides with highsequence identity to the codon-altered CS02, CS03, CS04, CS05, and CS06constructs. In some embodiments, these sequences include significantlyfewer CpG dinucleotides, as compared to wild type constructs, as is morefully described below.

Advantageously, the CS02, CS03, CS04, CS05, and CS06 codon-alteredFactor IX sequences described herein provide superior Factor IXexpression in vivo, as compared to equivalent wild-type sequences. Forexample, Example 1 shows that self-complementary AAV vectors carrying aCS02, CS03, CS04, CS05, or CS06 codon-altered Factor IX(R384L) codingsequence provide 20-fold to 40-fold increases in Factor IX activity invivo, relative to a self-complementary AAV vector carrying a wild-typeFactor IX coding sequence. Similarly, 2-fold to 4-fold increases areseen in Factor IX expression relative to a self-complementary AAV vectorcarrying a wild-type Factor IX(R384L) coding sequence (Table 2).

Advantageously, the improved Factor IX activity generated from the CS02,CS03, CS04, CS05, and CS06 codon altered sequences can be furtherenhanced by introducing one or more copies of a liver-specificregulatory element upstream of the Factor IX coding sequence. Forexample, as demonstrated in Examples 2 and 3, inclusion of one or moreliver-specific CRM8 regulatory control elements in theself-complementary AAV Factor IX vector further increased Factor IXexpression 2-fold to 3-fold in a mouse model and 2-fold to 13-fold inhuman hepatocytes (Tables 3 and 4, respectively). Likewise, inclusion ofone or more copies of a liver-specific CRM8 regulatory control elementin a single-stranded AAV Factor IX vector increased Factor IX activity2-fold in vivo (mouse model; Table 5) and up to 26-fold in humanhepatocytes (Table 6).

Surprisingly, while self-complementary AAV vectors encoding acodon-altered Factor IX polypeptide lacking liver-specific CRM8regulatory control elements provided greater increases in Factor IXexpression than similar single-stranded AAV vectors (compare the6.2-fold increase in FIX activity provided by CS06-CRM.0-scV with the3.9-fold increase in Factor IX activity provided by CS06-CRM.0-ssV (SEQID NO:40) in Table 6), single-stranded AAV Factor IX vectors containingmultiple copies of the liver-specific CRM8 regulatory control elementssignificantly outperformed similar self-complementary AAV vectors(compare the 12.8-fold increase in Factor IX activity provided byCS02-CRM8.3-scV, relative to CS02-CRM8.0-scV, in Table 4 to the16.8-fold increase in Factor IX activity provided by CS06-CRM8.3-ssV(SEQ ID NO:40), relative to CS06-CRM8.0-scV, in Table 6).

II. Definitions

As used herein, the following terms have the meanings ascribed to themunless specified otherwise.

As used herein, the terms “Factor IX” and “FIX” (with the “IX” referringto the Roman numerals to mean “nine”) are used interchangeably, andrefer to any protein with Factor IX activity (e.g., active FIX, oftenreferred to as “FIXa”) or a protein precursor (e.g., a pro-protein or apre-pro-protein, often referred to as pFIX and ppFIX) of a protein withFactor IX activity, particularly Factor X cleavage activity in thepresence of Factor VIII, e.g., as measured using the one stage Factor IXclotting assay described in Chapter 2.7.11 of the European Pharmacopoeia9.0, the content of which is hereby incorporated by reference.

Factor IX is translated as an inactive, single-chain polypeptide thatincludes a signal peptide, a propeptide, a light chain, an activationpeptide, and a heavy chain, often referred to as a Factor IXpre-pro-polypeptide. The Factor IX pre-pro-peptide undergoespost-translational processing to form an active Factor IX protein (e.g.,FIXa). This processing includes removal (e.g., by cleavage) of thesignal peptide, followed by removal (e.g., by cleavage) of thepropeptide, to form a single-chain mature Factor IX polypeptide,containing the Factor IX light chain and Factor IX heavy chain, which isstill inactive. The mature Factor IX polypeptide is further cleaved toexcise the activation peptide between the Factor IX light chain andFactor IX heavy chain, forming an active Factor IX protein (e.g., FIXa).The Factor IX light chain and Factor IX light chain remain associatedthrough a disulfide bond.

For example, the wild type human Factor IX pre-pro-protein is firstcleaved to release the encoded signal peptide (amino acids 1-28 ofFIX-FL-AA (SEQ ID NO:2)), forming a first single-chain pro-protein. Thissingle-chain pro-peptide is then cleaved to release the propeptide(amino acids 29-46 of FIX-FL-AA (SEQ ID NO:2)) to form a secondsingle-chain pro-protein (e.g., FIX-MP-AA (SEQ ID NO: 10), with the “MP”designation standing for “mature protein”). The second single-chainpro-protein is then cleaved twice between the FIX light chain and FIXheavy chain, by Factor XIa, to release an activation peptide (aminoacids 192-226 of FIX-FL-AA (SEQ ID NO:2)). This forms the active FactorIXa protein consisting of separate light and heavy chains associatedthrough a disulfide bond. For additional information on the structure,function, and activation of Factor IX see, e.g., Brandstetter H. et al.P.N.A.S. USA, 92(21):9796-800 (1995), Hopfner K P et al., Structure,7(8):989-96 (1999), and Gailani D. et al., Thromb Res., 133 Suppl1:S48-51 (2014), the contents of which are incorporated herein byreference, in their entireties, for all purposes.

As described herein, this active Factor IXa protein can include one ormore variants, with the R338L variant finding particular use in someembodiments. This is referred to as “FIXp-MP-AA” (SEQ ID NO: 12) withthe nucleic acid sequence being referred to herein as “FIXp-MP-NA”; the“FIXp” stands for the inclusion of the Padua R338L variant in the finalprotein. It should be noted that codon-optimized sequences CS02-CS06,exemplified herein, encode the FIXp protein, including the R338Lvariant. Thus, specifically included in the definition of FIX is FIXp.

As used herein, the terms “Factor IX polypeptide” and “FIX polypeptide”refer to a polypeptide having Factor IX serine protease activity underparticular conditions, e.g., as measured using the one stage Factor IXclotting assay described in Chapter 2.7.11 of the European Pharmacopoeia9.0. Factor IX polypeptides include single-chain precursor polypeptides(including Factor IX pre-pro-polypeptides, Factor IX pro-peptides, andmature, single-chain Factor IX polypeptides) which, when activated bythe post-translational processing described above, become active FactorIX protein with Factor IX serine protease activity, as well as theactive Factor IX proteins, themselves. Specifically included in thedefinition of Factor IX polypeptides are Factor IX polypeptidesincluding the R338L variant. In an exemplary embodiment, a human FactorIX polypeptide refers to a polypeptide that includes an amino acidsequence with high sequence identity (e.g., at least 85%, 90%, 95%, 99%,or more) to the portion of the wild type human Factor IX polypeptidethat includes the light and heavy chains, FIX-MP-AA (SEQ ID NO:10, shownin FIG. 11A) or to the portion of the padua human Factor IX polypeptidethat includes the light and heavy chains, FIXp-MP-AA (SEQ ID NO: 12,shown in FIG. 12).

As used herein, the terms “Factor IX light chain,” or simply “lightchain,” refer to the polypeptide in an activated Factor IXa proteinderived from the N-terminal portion of the Factor IX single-chainpolypeptide, containing the Gla module, EGF-like 1, and EGF-like 2domains of Factor IX. In an exemplary embodiment, amino acids 47-191 ofthe human pre-pro-Factor IX polypeptide (FIX-FL-AA (SEQ ID NO:2))constitute a Factor IX light chain. As used herein, the amino acidsequence of the wild-type Factor IX light chain is referred to asFIX-LC-AA (SEQ ID NO:62).

As used herein, the term “Factor IX heavy chain,” or simply “heavychain,” refers to the polypeptide in an activated Factor IXa proteinderived from the C-terminal portion of the Factor IX single-chainpolypeptide, containing the peptidase S1 domain of Factor IX. In anexemplary embodiment, amino acids 227-461 of the human pre-pro-Factor IXpolypeptide (FIX-FL-AA (SEQ ID NO:2)) constitute a Factor IX heavychain. As used herein, the amino acid sequence of the wild-type FactorIX heavy chain is referred to as FIX-HC-AA (SEQ ID NO:63) and FIXp-HC-AA(SEQ ID NO:64) when the R338L variant is included.

Generally, Factor IX light and heavy chains are expressed as a singlepolypeptide chain, e.g., along with an activation peptide. However, insome embodiments, a Factor IX light chain and Factor VIII heavy chainare expressed as separate polypeptide chains (e.g., co-expressed), andreconstituted to form a Factor IX protein (e.g., in vivo or in vitro).In general, for the purposes of the present invention, even if twochains are expressed separately, they are generally on the sameexpression vector (e.g. the viral genome), rather than on differentexpression vectors.

As used herein, the term “Factor IX activation peptide,” or simply“activation peptide,” refers to the peptide excised from a Factor IXsingle-chain polypeptide upon activation of the Factor IXa protein. Inan exemplary embodiment, amino acids 192-226 of the human pre-pro-FactorIX polypeptide (FIX-FL-AA (SEQ ID NO:2)) constitute a Factor IXactivation peptide. As used herein, the amino acid sequence of thewild-type Factor IX activation peptide is referred to as FIX-AP-AA (SEQID NO:56).

As used herein, the term “Factor IX signal peptide,” or simply “signalpeptide,” refers to the peptide excised from the N-terminus of a FactorIX pre-pro-polypeptide by a signal peptidase. The signal peptide directsnewly translated Factor IX pre-pro-protein to the endoplasmic reticulum.In an exemplary embodiment, amino acids 1-28 of the human pre-pro-FactorIX polypeptide (FIX-FL-AA (SEQ ID NO:2)) constitute a Factor IX signalpeptide. As used herein, the amino acid sequence of the wild-type FactorIX signal peptide is referred to as FIX-SP-AA (SEQ ID NO:37). A numberof signal peptides of the invention are shown in FIGS. 19 and 22.

As used herein, the term “Factor IX pro-peptide,” or simply“pro-peptide,” refers to the peptide excised from the N-terminus of aFactor IX pro-polypeptide (e.g., after cleavage of the signal peptide)by Furin. The pro-peptide includes a γ-carboxylation recognition sitethat recruits carboxylase to the adjacent Gla module, thereby promotingcarboxylation of glutamine residues. In an exemplary embodiment, aminoacids 29-46 of the human pre-pro-Factor IX polypeptide (FIX-FL-AA (SEQID NO:2)) constitute a Factor IX pro-peptide. As used herein, the aminoacid sequence of the wild-type Factor IX pro-peptide is referred to asFIX-PP-AA (SEQ ID NO:38).

As used herein, the term “Factor IX pre-pro-peptide,” or simply“pre-pro-peptide,” refers to the aggregate of the Factor IX signalpeptide and pro-polypeptide. In an exemplary embodiment, amino acids1-46 of the human pre-pro-Factor IX polypeptide (FIX-FL-AA (SEQ IDNO:2)) constitute a Factor IX pre-pro-peptide. As used herein, the aminoacid sequence of the wild-type Factor IX pre-pro-peptide is referred toas FIX-PPP-AA (SEQ ID NO:36) with the nucleic acid sequence, shown inFIG. 18, referred to as FIX-PPP-NA (SEQ ID NO: 18) (with thecorresponding FIXp-PPP-AA and FIXp-PPP-NA when the R338L variant isused).

Unless otherwise specified herein, the numbering of Factor IX aminoacids refers to the corresponding amino acid in the full-length,wild-type human Factor IX pre-pro-polypeptide sequence (FIX-FL-AA),presented as SEQ ID NO:2 in FIG. 3A. As such, when referring to an aminoacid substitution in a Factor IX polypeptide disclosed herein, therecited amino acid number refers to the analogous (e.g., structurally orfunctionally equivalent) and/or homologous (e.g., evolutionarilyconserved in the primary amino acid sequence) amino acid in thefull-length, wild-type Factor IX pre-pro-polypeptide sequence. Forexample, an R384L amino acid substitution refers to an R to Lsubstitution at position 384 of the full-length, wild-type human FactorIX pre-pro-peptide sequence (FIX-FL-AA (SEQ ID NO:2)), an R to Lsubstitution at position 338 of the mature, wild-type Factor IXsingle-chain polypeptide (FIX-MP-AA (SEQ ID NO:10), an R to Lsubstitution at position 346 of the full-length, wild-type human FactorIX pre-pro-peptide isoform 2 sequence (FIX2-FL-AA (SEQ ID NO:3)), an Rto L substitution at position 300 of the mature, wild-type human FactorIX pre-pro-peptide isoform 2 sequence (FIX2-FL-AA (SEQ ID NO:3)), and anR to L substitution at position 158 of the wild-type human Factor IXheavy chain sequence (FIX-HC-AA (SEQ ID NO:63)). Thus, all of thesenomenclatures describe the same “Padua” amino acid substitution, indifferent Factor IX constructs.

As described herein, the Factor IX amino acid numbering system isdependent on whether the Factor IX pre-pro-peptide (e.g., amino acids1-46 of the full-length, wild-type human Factor IX sequence, inclusiveof the signal peptide and pro-peptide) is included. Where thepre-pro-peptide is included, the numbering is referred to as“pre-pro-peptide inclusive” or “PPI”. Where the pre-pro-peptide is notincluded, the numbering is referred to as “pre-pro-peptide exclusive” or“PPE.” For example, R384L is PPI numbering for the same amino acidsubstitution as R338L, in PPE numbering. Similarly, the Factor IX aminoacid numbering is also dependent upon the Factor IX isoform. Forexample, R384L is isoform 1 numbering for the same amino acidsubstitution as R346L, in isoform 2 numbering. Unless otherwiseindicated, all amino acid numbering refers to the corresponding aminoacid in the full-length, wild-type human Factor IX isoform 1 sequence(FIX-FL-AA), presented as SEQ ID NO:2 in FIG. 3A. This numbering isidentical for the FIXp-FL-AA (SEQ ID NO:4), which has the same aminoacid sequence, aside from the R384L “Padua” mutation.

Non-limiting examples of wild type Factor IX polypeptides include humanpre-pro-Factor IX (e.g., GenBank accession nos. NP_000124.1 (FIX-FL-AA(SEQ ID NO:2)) and NP_001300842.1 (FIX2-FL-AA (SEQ ID NO:3)),corresponding single chain Factor IX lacking the signal peptide (aminoacids 1-28 of the pre-pro-protein) and/or propeptide (amino acids 29-46of the pre-pro-protein), and natural variants thereof; porcinepre-pro-Factor IX (e.g., UniProt accession no. P00741), correspondingsingle chain Factor IX lacking the signal peptide, and natural variantsthereof, murine pre-pro-Factor IX (e.g., UniProt accession no. P16294),corresponding single chain Factor IX lacking the signal peptide, andnatural variants thereof; rat pre-pro-Factor IX (e.g., UniProt accessionno. P16296), corresponding single chain Factor IX lacking the signalpeptide, and natural variants thereof; and other mammalian Factor VIIIhomologues (e.g., chimpanzee, ape, hamster, guinea pig, etc.).

As used herein, a Factor IX polypeptide includes natural variants andartificial constructs with Factor X cleavage activity in the presence ofFactor VIII. As used in the present disclosure, Factor IX encompassesany natural variants, alternative sequences, isoforms, or mutantproteins that retain some basal Factor IX cleavage activity (e.g., atleast 5%, 10%, 25%, 50%, 75%, or more of the corresponding wild typeactivity as assayed in a one stage clotting assay according to Chapter2.7.11 of the European Pharmacopoeia 9.0, which is specificallyincorporated herein by reference for its teachings of the Assay of HumanCoagulation Factor IX in chapter 2.7.11. Examples of Factor IX aminoacid variations (relative to FIX-FL-AA (SEQ ID NO:2)) found in the humanpopulation include, without limitation, I17N, L20S, C28R, C28Y, V30I,R43L, R43Q, R43W, K45N, R46S, R46T, N48I, S49P, L52S, E53A, E54D, E54G,F55C, G58A, G58E, G58R, E66V, E67K, F71S, E73K, E73V, R75Q, E79D, T84R,Y91C, D93G, Q96P, C97S, P101R, C102R, C102R, G106D, G106S, C108S, D110N,I112S, N113K, Y115C, C119F, C119R, E124K, G125E, G125R, G125V, C134Y,I136T, N138H, G139D, G139S, C155F, G160E, Q167H, S169C, C170F, C178R,C178W, R191C, R191H, R226G, R226Q, R226W, V227D, V227F, V228F, V228L,Q241H, Q241K, C252S, C252Y, G253E, G253R, A265T, C268W, A279T, N283D,E291V, R294G, R294Q, V296M, H302R, N306S, I316F, L318R, L321Q, N328K,N328Y, P333H, P333T, T342K, T342M, I344L, G351D, W356C, G357E, G357R,K362E, G363W, A366D, R379G, R379Q, C382Y, L392F, L383I, R384L, K387E,I390F, M394K, F395I, F395L, C396F, C396S, A397P, R404T, C407R, C407S,D410H, S411G, S411I, G412E, G413R, P414T, V419E, F424V, T426P, S430T,W431G, W431R, G432S, E433A, G433K, C435Y, A436V, G442E, G442R, I443T,R449Q, R449W, Y450C, W453R, and I454T. As discussed more fully below,this numbering is relative to the wild type human FIX. Other amino acidvariations identified in the human population are known and can befound, for example, using the National Center for BiotechnologyInformation's (“NCBI”) variation viewer, accession numberGCF_000001405.25. Factor VIII proteins also include polypeptidescontaining post-translational modifications.

Of particular use in the present disclosure is a FIX protein thatincludes the so called “Padua” mutation, an arginine to leucine changeat position 338 of the mature single-strand Factor IX protein (R338L),position 384 of the Factor IX pre-pro-polypeptide (R384L). This mutationconfers hyperfunctional activity to the FIX protein. For example, it wasshown that “Padua” protein (e.g., Factor IX containing the R338Lmutation) is 5-fold to 10-fold more active than wild-type Factor IX invivo. U.S. Pat. No. 6,531,298; Simioni P. et al., N Engl J Med. 361(17):1671-75 (2009), hereby incorporated by reference in its entirety.Accordingly, the disclosure provides amino acid and nucleic acidconstructs that encode a Padua-FIX protein, sometimes referred to hereinas “FIXp” or “pFIX”.

As used herein, the terms “Factor IX polynucleotide” and “FIXpolynucleotide” refer to a polynucleotide encoding a Factor IXpolypeptide having Factor IX serine protease activity under particularconditions, e.g., as measured using the one stage Factor IX clottingassay described in Chapter 2.7.11 of the European Pharmacopoeia 9.0.Factor IX polynucleotides include polynucleotides encoding Factor IXsingle-chain precursor polypeptides, including Factor IXpre-pro-polypeptides, Factor IX pro-peptides, and mature, single-chainFactor IX polypeptides, which, when activated by the post-translationalprocessing described above, become active Factor IX protein with FactorIX serine protease activity. Specifically included in the definition ofFactor IX polynucleotides are polynucleotides encoding a Factor IXpolypeptide that includes the R338L variant. In an exemplary embodiment,a human Factor IX polynucleotide refers to a polynucleotide that encodesa polypeptide that includes an amino acid sequence with high sequenceidentity (e.g., at least 85%, 90%, 95%, 99%, or more) to the portion ofthe wild type human Factor IX polypeptide that includes the light andheavy chains, FIX-MP-AA (SEQ ID NO: 10, shown in FIG. 11A) or to theportion of the padua human Factor IX polypeptide that includes the lightand heavy chains, FIXp-MP-AA (SEQ ID NO: 12, shown in FIG. 12).

As described herein, Factor IX polynucleotides can include regulatoryelements, such as promoters, enhancers, terminators, polyadenylationsequences, and introns, as well viral packaging elements, such asinverted terminal repeats (“ITRs”), and/or other elements that supportreplication of the polynucleotide in a non-viral host cell, e.g., areplicon supporting propagation of the polynucleotide, e.g., in abacterial, yeast, or mammalian host cell.

Of particular use in the present disclosure are codon-altered Factor IXpolynucleotides. As described herein, the codon-altered FIXpolynucleotides provide increased expression of transgenic Factor IX invivo, as compared to the level of Factor IX expression provided by anatively-coded Factor IX construct (e.g., a polynucleotide encoding thesame Factor IX amino acid sequence using the wild-type human codons). Asused herein, the term “increased expression” refers to an increasedlevel of transgenic Factor IX protein in the blood of an animaladministered the codon-altered polynucleotide encoding Factor IX, ascompared to the level of transgenic Factor IX protein in the blood of ananimal administered a natively-coded Factor IX construct. Increasedexpression of the protein leads to an increase in Factor IX activity;thus, increased expression leads to increased activity.

In some embodiments, increased expression refers to at least 25% greatertransgenic Factor IX polypeptide in the blood of an animal administeredthe codon-altered Factor IX polynucleotide, as compared to the level oftransgenic Factor IX polypeptide in the blood of an animal administereda natively-coded Factor IX polynucleotide. For the purpose of thepresent disclosure, increased expression refers to an effect generatedby the alteration of the codon sequence, rather than hyperactivitycaused by an underlying amino acid substitution, e.g., a “Padua”mutation. That is, the expression level obtained from a codon-optimizedsequence encoding a “Padua” Factor IX polynucleotide is comparedrelative to the expression level obtained from a natively-coded “Padua”protein. In some embodiments, increased expression refers to at least50% greater, at least 75% greater, at least 100% greater, at least3-fold greater, at least 4-fold greater, at least 5-fold greater, atleast 6-fold greater, at least 7-fold greater, at least 8-fold greater,at least 9-fold greater, at least 10-fold greater, at least 15-foldgreater, at least 20-fold greater, at least 25-fold greater, at least30-fold greater, at least 40-fold greater, at least 50-fold greater, atleast 60-fold greater, at least 70-fold greater, at least 80-foldgreater, at least 90-fold greater, at least 100-fold greater, at least125-fold greater, at least 150-fold greater, at least 175-fold greater,at least 200-fold greater, at least 225-fold greater, or at least250-fold greater transgenic Factor IX polypeptide in the blood of ananimal administered the codon-altered Factor IX polynucleotide, ascompared to the level of transgenic Factor IX polypeptide in the bloodof an animal administered a natively coded Factor IX polynucleotide.Factor IX polypeptide levels in the blood of an animal can be measured,for example, using an ELISA assay specific for Factor IX polypeptide.

By “Factor IX activity” or “Factor IX serine protease activity” hereinis meant the ability to cleave a Factor X polypeptide in the presence ofa Factor VIIIa co-factor, e.g., via hydrolysis of the Arg194-Ile195peptide bond in wild-type Factor IX, thus activating Factor X to FactorXa. The activity levels can be measured using any Factor IX activityknown in the art; suitable assays are outlined herein; an exemplaryassay for determining Factor IX activity is the one stage Factor IXclotting assay described in Chapter 2.7.11 of the European Pharmacopoeia9.0, used in the examples provided herein. In some embodiments, humanplasma deficient of FIX activity is used as a control in the one stageclotting assay to determine the Factor IX specificity.

Because certain Factor IX variants have enhanced specific activities ascompared to wild type Factor IX in vivo, e.g., the human ‘Padua’ varianthas 5-fold to 10-fold greater Factor IX serine protease activity thandoes natively-coded type human Factor IX, in some embodiments, thetherapeutic potential of a Factor IX polynucleotide composition isevaluated by the increase in Factor IX activity in the blood of ananimal administered a Factor IX polynucleotide, e.g., instead of or inaddition to increased Factor IX expression. In some embodiments, as usedherein, increased Factor IX activity refers to a greater increase inFactor IX activity in the blood of an animal administered acodon-altered Factor IX polynucleotide, relative to a baseline Factor IXactivity in the blood of the animal prior to administration of thecodon-altered Factor IX polynucleotide, as compared to the increase inFactor IX activity in the blood of an animal administered anatively-coded Factor IX polynucleotide, relative to a baseline FactorIX activity in the blood of the animal prior to administration of thenatively-coded Factor IX polynucleotide. In some embodiments, increasedFactor IX activity refers to at least a 25% greater increase in FactorIX activity in the blood of an animal administered the codon-alteredFactor IX polynucleotide, relative to a baseline level of Factor IXactivity in the blood of the animal prior to administration of thecodon-altered Factor IX polynucleotide, as compared to the increase inthe level Factor IX activity in the blood of an animal administered anatively-coded Factor IX polynucleotide, relative to the baseline levelof Factor IX activity in the animal prior to administration of thenatively-coded Factor IX polynucleotide. In some embodiments, increasedFactor IX activity refers to at least 50% greater, at least 75% greater,at least 100% greater, at least 3-fold greater, at least 4-fold greater,at least 5-fold greater, at least 6-fold greater, at least 7-foldgreater, at least 8-fold greater, at least 9-fold greater, at least10-fold greater, at least 15-fold greater, at least 20-fold greater, atleast 25-fold greater, at least 30-fold greater, at least 40-foldgreater, at least 50-fold greater, at least 60-fold greater, at least70-fold greater, at least 80-fold greater, at least 90-fold greater, atleast 100-fold greater, at least 125-fold greater, at least 150-foldgreater, at least 175-fold greater, at least 200-fold greater, at least225-fold greater, or at least 250-fold greater increase in Factor IXactivity in the blood of an animal administered the codon-altered FactorIX polynucleotide, relative to a baseline level of Factor IX activity inthe blood of the animal prior to administration of the codon-alteredFactor IX polynucleotide, as compared to the increase in the levelFactor IX activity in the blood of an animal administered anatively-coded Factor IX polynucleotide, relative to the baseline levelof Factor IX activity in the animal prior to administration of thenatively-coded Factor IX polynucleotide. Activity is measured using theone stage Factor IX clotting assay described in Chapter 2.7.11 of theEuropean Pharmacopoeia 9.0, as described herein.

As used herein, the term “hemophilia” refers to a group of diseasestates broadly characterized by reduced blood clotting or coagulation.Hemophilia may refer to Type A, Type B, or Type C hemophilia, or to thecomposite of all three diseases types. Type A hemophilia (hemophilia A)is caused by a reduction or loss of factor VIII (FVIII) activity and isthe most prominent of the hemophilia subtypes. Type B hemophilia(hemophilia B) results from the loss or reduction of factor IX (FIX)clotting function. Type C hemophilia (hemophilia C) is a consequence ofthe loss or reduction in factor XI (FXI) clotting activity. Hemophilia Aand B are X-linked diseases, while hemophilia C is autosomal.Conventional treatments for hemophilia include both prophylactic andon-demand administration of clotting factors, such as FVIII, FIX,including Bebulin®-VH, and FXI, as well as FEIBA-VH, desmopressin, andplasma infusions.

As used herein, the term “Factor IX gene therapy,” or “FIX genetherapy,” includes any therapeutic approach of providing a nucleic acidencoding Factor IX to a patient to relieve, diminish, or prevent thereoccurrence of one or more symptoms (e.g., clinical factors) associatedwith a Factor IX deficiency (e.g., hemophilia B). The term encompassesadministering any compound, drug, procedure, or regimen comprising anucleic acid encoding a Factor IX molecule, including any modified formof Factor IX (e.g., a Factor VIII R384L variant), for maintaining orimproving the health of an individual with a Factor IX deficiency (e.g.,hemophilia B). One skilled in the art will appreciate that either thecourse of FIX gene therapy or the dose of a FIX gene therapy therapeuticagent can be changed, e.g., based upon the results obtained inaccordance with the present disclosure.

The terms “therapeutically effective amount or dose” or “therapeuticallysufficient amount or dose” or “effective or sufficient amount or dose”refer to a dose that produces therapeutic effects for which it isadministered. For example, a therapeutically effective amount of a druguseful for treating hemophilia can be the amount that is capable ofpreventing or relieving one or more symptoms associated with hemophilia.

In some embodiments, a therapeutically effective treatment results in adecrease in the frequency and/or severity of bleeding incidents in asubject.

As used herein, the term “gene” refers to the segment of a DNA moleculethat codes for a polypeptide chain (e.g., the coding region). In someembodiments, a gene is positioned by regions immediately preceding,following, and/or intervening the coding region that are involved inproducing the polypeptide chain (e.g., regulatory elements such as apromoter, enhancer, polyadenylation sequence, 5′-untranslated region,3′-untranslated region, or intron).

As used herein, the term “regulatory elements” refers to nucleotidesequences, such as promoters, enhancers, terminators, polyadenylationsequences, introns, etc., that provide for the expression of a codingsequence in a cell.

As used herein, the term “promoter element” refers to a nucleotidesequence that assists with controlling expression of a coding sequence.Generally, promoter elements are located 5′ of the translation startsite of a gene. However, in certain embodiments, a promoter element maybe located within an intron sequence, or 3′ of the coding sequence. Insome embodiments, a promoter useful for a gene therapy vector is derivedfrom the native gene of the target protein (e.g., a Factor VIIIpromoter). In some embodiments, a promoter useful for a gene therapyvector is specific for expression in a particular cell or tissue of thetarget organism (e.g., a liver-specific promoter). In yet otherembodiments, one of a plurality of well characterized promoter elementsis used in a gene therapy vector described herein. Non-limiting examplesof well-characterized promoter elements include the CMV early promoter,the β-actin promoter, and the methyl CpG binding protein 2 (MeCP2)promoter. In some embodiments, the promoter is a constitutive promoter,which drives substantially constant expression of the target protein. Inother embodiments, the promoter is an inducible promoter, which drivesexpression of the target protein in response to a particular stimulus(e.g., exposure to a particular treatment or agent). For a review ofdesigning promoters for AAV-mediated gene therapy, see Gray et al.(Human Gene Therapy 22:1143-53 (2011)), the contents of which areexpressly incorporated by reference in their entirety for all purposes.

As used herein, a “CRM8” element refers to cis-acting regulatory modulederived from the SERPINA1 gene (NCBI accession number NM_000295.4) thatenhances expression of an operatively linked gene, e.g., a sequenceencoding a Factor IX polypeptide, in a liver-specific fashion havinghigh sequence identity to SEQ ID NO:39. As used herein, a CRM8 elementrefers to a single copy of the regulatory element which, in someembodiments, is included in one or more copies within a Factor IXpolynucleotide, e.g., 1, 2, 3, or more copies. For further informationon CRM elements, such as CRM8, see Chuah M K et al., Mol Ther.,22(9):1605-13 (2014), which is hereby incorporated by reference.

As used herein an “MVM intron” refers to an intron sequence derived fromminute virus of mice having high sequence identity to SEQ ID NO:53. Forfurther information on the MVM intron itself, see Haut and Pintel, JVirol. 72(3):1834-43 (1998), and use of the MVM intron in AAV genetherapy vectors, see Wu Z et al., Mol Ther., 16(2):280-9 (2008), both ofwhich are hereby incorporated by reference.

As used herein, the term “operably linked” refers to the relationshipbetween a first reference nucleotide sequence (e.g., a gene) and asecond nucleotide sequence (e.g., a regulatory control element) thatallows the second nucleotide sequence to affect one or more propertiesassociated with the first reference nucleotide sequence (e.g., atranscription rate). In the context of the present disclosure, aregulatory control element is operably linked to a Factor IX transgenewhen the regulatory element is positioned within a gene therapy vectorsuch that it exerts an affect (e.g., a promotive or tissue selectiveaffect) on transcription of the Factor IX transgene.

As used herein, the term “vector” refers to any nucleic acid constructused to transfer a Factor IX nucleic acid into a host cell. In someembodiments, a vector includes a replicon, which functions to replicatethe nucleic acid construct. Non-limiting examples of vectors useful forgene therapy include plasmids, phages, cosmids, artificial chromosomes,and viruses, which function as autonomous units of replication in vivo.In some embodiments, a vector is a viral vector for introducing a FactorIX nucleic acid into the host cell. Many modified eukaryotic virusesuseful for gene therapy are known in the art. For example,adeno-associated viruses (AAVs) are particularly well suited for use inhuman gene therapy because humans are a natural host for the virus, thenative viruses are not known to contribute to any diseases, and theviruses illicit a mild immune response.

As used herein, the term “Factor IX viral vector” refers to arecombinant virus comprising a Factor IX polynucleotide, encoding aFactor IX polypeptide, which is sufficient for expression of the FactorIX polypeptide when introduced into a suitable animal host (e.g., ahuman). Specifically included within the definition of Factor IX viralvector are recombinant viruses in which a codon-altered Factor IXpolynucleotide, which encodes a Factor IX polypeptide, has been insertedinto the genome of the virus. Also specifically included within thedefinition of Factor IX viral vectors are recombinant viruses in whichthe native genome of the virus has been replaced with a Factor IXpolynucleotide, which encodes a Factor IX polypeptide. Included withinthe definition of Factor IX viral vectors are recombinant virusescomprising a Factor IX polynucleotide, which encodes a “Padua” variantof Factor IX.

As used herein, the term “Factor IX viral particle” refers to a viralparticle encapsulating a Factor IX polynucleotide, encoding a Factor IXpolypeptide, which is specific for expression of the Factor IXpolypeptide when introduced into a suitable animal host (e.g., a human).Specifically included within the definition of Factor IX viral particlesare recombinant viral particles encapsulating a genome in which acodon-altered Factor IX polynucleotide, which encodes a Factor IXpolypeptide, has been inserted. Also specifically included within thedefinition of Factor IX viral particles are recombinant viral particlesencapsulating a Factor IX polynucleotide, which encodes a Factor IXpolypeptide, which replaces the natice genome of the virus. Includedwithin the definition of Factor IX viral particles are recombinant viralparticles encapsulating a Factor IX polynucleotide, which encodes a“Padua” variant of Factor IX.

By “AAV” or “adeno-associated virus” herein is meant a Dependoparvoviruswithin the Parvoviridae genus of viruses. As used herein, AAV can referto a virus derived from a naturally occurring “wild-type” AAV genomeinto which a Factor IX polynucleotide has been inserted, a recombinantvirus derived from a recombinant Factor IX polynucleotide packaged intoa capsid using capsid proteins encoded by a naturally occurring AAV capgene, or a recombinant virus derived from a recombinant Factor IXpolynucleotide packaged into a capsid using capsid proteins encoded by anon-natural capsid cap gene. Included within the definition of AAV areAAV type 1 (AAV1), AAV type 2 (AAV2), AAV type 3 (AAV3), AAV type 4(AAV4), AAV type 5 (AAV5), AAV type 6 (AAV6), AAV type 7 (AAV7), AAVtype 8 (AAV8), and AAV type 9 (AAV9) viruses encapsulating a Factor IXpolynucleotide and viruses formed by one or more variant AAV capsidproteins encapsulating a Factor IX polynucleotide.

By “AAV8,” “AAV-8,” or “AAV serotype 8” herein is meant a virus formedby an AAV8 capsid viral protein that encapsulates a Factor IXpolynucleotide.

As used herein, the term “CpG” refers to a cytosine-guanine dinucleotidealong a single strand of DNA, with the “p” representing the phosphatelinkage between the two.

As used herein, the term “CpG island” refers to a region within apolynucleotide having a statistically elevated density of CpGdinucleotides. As used herein, a region of a polynucleotide (e.g., apolynucleotide encoding a codon-altered Factor IX protein) is a CpGisland if, over a 200-base pair window: (i) the region has GC content ofgreater than 50%, and (ii) the ratio of observed CpG dinucleotides perexpected CpG dinucleotides is at least 0.6, as defined by therelationship:

$\frac{{N\lbrack{CpG}\rbrack}*{N\left\lbrack {{length}\mspace{14mu} {of}\mspace{14mu} {window}} \right\rbrack}}{{N\lbrack C\rbrack}*{N\lbrack G\rbrack}} \geq {0.6.}$

For additional information on methods for identifying CpG islands, seeGardiner-Garden M. et al., J Mol Biol., 196(2):261-82 (1987), thecontent of which is expressly incorporated herein by reference, in itsentirety, for all purposes.

As used herein, the term “nucleic acid” refers to deoxyribonucleotidesor ribonucleotides and polymers thereof in either single- ordouble-stranded form, and complements thereof. The term encompassesnucleic acids containing known nucleotide analogs or modified backboneresidues or linkages, which are synthetic, naturally occurring, andnon-naturally occurring, which have similar binding properties as thereference nucleic acid, and which are metabolized in a manner similar tothe reference nucleotides. Examples of such analogs include, withoutlimitation, phosphorothioates, phosphoramidates, methyl phosphonates,chiral-methyl phosphonates, 2-O-methyl ribonucleotides, andpeptide-nucleic acids (PNAs). However, particularly useful embodimentsherein, for use in gene therapy in patients, use phosphodiester bonds.

By “nucleic acid compositions” herein is meant any molecule orformulation of a molecule that includes a Factor IX polynucleotide,encoding a Factor IX polynucleotide. Included within the definition ofnucleic acid compositions are Factor IX polynucleotides, aqueoussolutions of Factor IX polynucleotides, viral particles encapsulating aFactor IX polynucleotide, and aqueous formulations of viral particlesencapsulating a Factor IX polynucleotide. A nucleic acid composition, asdisclosed herein, includes a codon-altered FIX gene, that encodes a FIXpolypeptide.

The term “amino acid” refers to naturally occurring and non-naturalamino acids, including amino acid analogs and amino acid mimetics thatfunction in a manner similar to the naturally occurring amino acids.Naturally occurring amino acids include those encoded by the geneticcode, as well as those amino acids that are later modified, e.g.,hydroxyproline, y-carboxyglutamate, and O-phosphoserine. Naturallyoccurring amino acids can include, e.g., D- and L-amino acids. As toamino acid sequences, one of ordinary skill in the art will recognizethat individual substitutions, deletions or additions to a nucleic acidor peptide sequence that alters, adds or deletes a single amino acid ora small percentage of amino acids in the encoded sequence is a“conservatively modified variant” where the alteration results in thesubstitution of an amino acid with a chemically similar amino acid.Conservative substitution tables providing functionally similar aminoacids are well known in the art. Such conservatively modified variantsare in addition to and do not exclude polymorphic variants, interspecieshomologs, and alleles of the disclosure.

Conservative amino acid substitutions providing functionally similaramino acids are well known in the art. Dependent on the functionality ofthe particular amino acid, e.g., catalytic, structural, or stericallyimportant amino acids, different groupings of amino acid may beconsidered conservative substitutions for each other. Table 1 providesgroupings of amino acids that are considered conservative substitutionsbased on the charge and polarity of the amino acid, the hydrophobicityof the amino acid, the surface exposure/structural nature of the aminoacid, and the secondary structure propensity of the amino acid.

TABLE 1 Groupings of conservative amino acid substitutions based on thefunctionality of the residue in the protein. Important FeatureConservative Groupings Charge/Polarity 1. H, R, and K 2. D and E 3. C,T, S, G, N, Q, and Y 4. A, P, M, L, I, V, F, and W Hydrophobicity 1. D,E, N, Q, R, and K 2. C, S, T, P, G, H, and Y 3. A, M, I, L, V, F, and WStructural/Surface Exposure 1. D, E, N, Q, H, R, and K 2. C, S, T, P, A,G, W, and Y 3. M, I, L, V, and F Secondary Structure Propensity 1. A, E,Q, H, K, M, L, and R 2. C, T, I, V, F, Y, and W 3. S, G, P, D, and NEvolutionary Conservation 1. D and E 2. H, K, and R 3. N and Q 4. S andT 5. L, I, and V 6. F, Y, and W 7. A and G 8. M and C

The terms “identical” or percent “identity,” in the context of two ormore nucleic acids or peptide sequences, refer to two or more sequencesor subsequences that are the same or have a specified percentage ofamino acid residues or nucleotides that are the same (i.e., about 60%identity, preferably 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, or higher identity over a specified region,when compared and aligned for maximum correspondence over a comparisonwindow or designated region) as measured using a BLAST or BLAST 2.0sequence comparison algorithms with default parameters described below,or by manual alignment and visual inspection.

As is known in the art, a number of different programs may be used toidentify whether a protein (or nucleic acid as discussed below) hassequence identity or similarity to a known sequence. Sequence identityand/or similarity is determined using standard techniques known in theart, including, but not limited to, the local sequence identityalgorithm of Smith & Waterman, Adv. Appl. Math., 2:482 (1981), by thesequence identity alignment algorithm of Needleman & Wunsch, J. Mol.Biol., 48:443 (1970), by the search for similarity method of Pearson &Lipman, Proc. Natl. Acad. Sci. U.S.A., 85:2444 (1988), by computerizedimplementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA inthe Wisconsin Genetics Software Package, Genetics Computer Group, 575Science Drive, Madison, Wis.), the Best Fit sequence program describedby Devereux et al., Nucl. Acid Res., 12:387-395 (1984), preferably usingthe default settings, or by inspection. Preferably, percent identity iscalculated by FastDB based upon the following parameters: mismatchpenalty of 1; gap penalty of 1; gap size penalty of 0.33; and joiningpenalty of 30, “Current Methods in Sequence Comparison and Analysis,”Macromolecule Sequencing and Synthesis, Selected Methods andApplications, pp 127-149 (1988), Alan R. Liss, Inc, all of which areincorporated by reference.

An example of a useful algorithm is PILEUP. PILEUP creates a multiplesequence alignment from a group of related sequences using progressive,pair wise alignments. It may also plot a tree showing the clusteringrelationships used to create the alignment. PILEUP uses a simplificationof the progressive alignment method of Feng & Doolittle, J. Mol. Evol.35:351-360 (1987); the method is similar to that described by Higgins &Sharp CABIOS 5:151-153 (1989), both incorporated by reference. UsefulPILEUP parameters including a default gap weight of 3.00, a default gaplength weight of 0.10, and weighted end gaps.

Another example of a useful algorithm is the BLAST algorithm, describedin: Altschul et al., J. Mol. Biol. 215, 403-410, (1990); Altschul etal., Nucleic Acids Res. 25:3389-3402 (1997); and Karlin et al., Proc.Natl. Acad. Sci. U.S.A. 90:5873-5787 (1993), both incorporated byreference. A particularly useful BLAST program is the WU-BLAST-2 programwhich was obtained from Altschul et al., Methods in Enzymology,266:460-480 (1996); http://blast.wustl/edu/blast/README.html].WU-BLAST-2 uses several search parameters, most of which are set to thedefault values. The adjustable parameters are set with the followingvalues: overlap span=1, overlap fraction=0.125, word threshold (T)=11.The HSP S and HSP S2 parameters are dynamic values and are establishedby the program itself depending upon the composition of the particularsequence and composition of the particular database against which thesequence of interest is being searched; however, the values may beadjusted to increase sensitivity.

An additional useful algorithm is gapped BLAST, as reported by Altschulet al., Nucl. Acids Res., 25:3389-3402, incorporated by reference.Gapped BLAST uses BLOSUM-62 substitution scores; threshold T parameterset to 9; the two-hit method to trigger ungapped extensions; charges gaplengths of k a cost of 10+k; Xu set to 16, and Xg set to 40 for databasesearch stage and to 67 for the output stage of the algorithms. Gappedalignments are triggered by a score corresponding to ˜22 bits.

A % amino acid sequence identity value is determined by the number ofmatching identical residues divided by the total number of residues ofthe “longer” sequence in the aligned region. The “longer” sequence isthe one having the most actual residues in the aligned region (gapsintroduced by WU-Blast-2 to maximize the alignment score are ignored).In a similar manner, “percent (%) nucleic acid sequence identity” withrespect to the coding sequence of the polypeptides identified is definedas the percentage of nucleotide residues in a candidate sequence thatare identical with the nucleotide residues in the coding sequence of thecell cycle protein. A preferred method utilizes the BLASTN module ofWU-BLAST-2 set to the default parameters, with overlap span and overlapfraction set to 1 and 0.125, respectively.

The alignment may include the introduction of gaps in the sequences tobe aligned. In addition, for sequences which contain either more orfewer amino acids than the protein encoded by the wild-type Factor IXsequence of FIG. 3A (SEQ ID NO:2), it is understood that in oneembodiment, the percentage of sequence identity will be determined basedon the number of identical amino acids or nucleotides in relation to thetotal number of amino acids or nucleotides. Thus, for example, sequenceidentity of sequences shorter than that shown in FIG. 3A (SEQ ID NO:2),as discussed below, will be determined using the number of nucleotidesin the shorter sequence, in one embodiment. In percent identitycalculations relative weight is not assigned to various manifestationsof sequence variation, such as, insertions, deletions, substitutions,etc.

In one embodiment, only identities are scored positively (+1) and allforms of sequence variation including gaps are assigned a value of “O”,which obviates the need for a weighted scale or parameters as describedbelow for sequence similarity calculations. Percent sequence identitymay be calculated, for example, by dividing the number of matchingidentical residues by the total number of residues of the “shorter”sequence in the aligned region and multiplying by 100. The “longer”sequence is the one having the most actual residues in the alignedregion.

The term “allelic variants” refers to polymorphic forms of a gene at aparticular genetic locus, as well as cDNAs derived from mRNA transcriptsof the genes, and the polypeptides encoded by them. The term “preferredmammalian codon” refers a subset of codons from among the set of codonsencoding an amino acid that are most frequently used in proteinsexpressed in mammalian cells as chosen from the following list: Gly(GGC, GGG); Glu (GAG); Asp (GAC); Val (GTG, GTC); Ala (GCC, GCT); Ser(AGC, TCC); Lys (AAG); Asn (AAC); Met (ATG); Ile (ATC); Thr (ACC); Trp(TGG); Cys (TGC); Tyr (TAT, TAC); Leu (CTG); Phe (TTC); Arg (CGC, AGG,AGA); Gln (CAG); His (CAC); and Pro (CCC).

As used herein, the term codon-altered refers to a polynucleotidesequence encoding a polypeptide (e.g., a Factor IX protein), where atleast one codon of the native polynucleotide encoding the polypeptidehas been changed to improve a property of the polynucleotide sequence.In some embodiments, the improved property promotes increasedtranscription of mRNA coding for the polypeptide, increased stability ofthe mRNA (e.g., improved mRNA half-life), increased translation of thepolypeptide, and/or increased packaging of the polynucleotide within thevector. Non-limiting examples of alterations that can be used to achievethe improved properties include changing the usage and/or distributionof codons for particular amino acids, adjusting global and/or local GCcontent, removing AT-rich sequences, removing repeated sequenceelements, adjusting global and/or local CpG dinucleotide content,removing cryptic regulatory elements (e.g., TATA box and CCAAT boxelements), removing of intron/exon splice sites, improving regulatorysequences (e.g., introduction of a Kozak consensus sequence), andremoving sequence elements capable of forming secondary structure (e.g.,stem-loops) in the transcribed mRNA.

As discussed herein, there are various nomenclatures to refer tocomponents of the disclosure herein. “CS-number” (e.g. “CS02,” “CS03,”“CS04,” “CS05,” “CS06,” etc.) refer to codon altered polynucleotidesencoding FIX polypeptides and/or the encoded polypeptides, includingvariants. For example, CS02-FL refers to the Full Length codon alteredCS02 polynucleotide sequence or amino acid sequence (sometimes referredto herein as “CS02-FL-AA” for the Amino Acid sequence and “CS02-FL-NA”(SEQ ID NO:5) for the Nucleic Acid sequence) encoded by the CS02polynucleotide sequence. Similarly, “CS02-LC” refers to either the codonaltered nucleic acid sequence (“CS02-LC-NA” (SEQ ID NO:42)) encoding thelight chain of a FIX polypeptide or the amino acid sequence (alsosometimes referred to herein as “CS02-LC-AA”) of the FIX light chainencoded by the CS02 polynucleotide sequence. Likewise, CS02-HC,CS02-HC-AA, and CS02-HC-NA (SEQ ID NO:41) are the same for the FIX heavychain. As will be appreciated by those in the art, for constructs suchas CS02, CS03, CS04, CS05, CS06, etc., that are only codon-altered (e.g.they do not contain additional amino acid substitutions as compared tothe Padua Factor IX variant), the amino acid sequences will beidentical, as the amino acid sequences are not altered by the codonoptimization. Thus, sequence constructs of the disclosure include, butare not limited to, CS02-FL-NA (SEQ ID NO:5), CS02-FL-AA, CS02-LC-NA(SEQ ID NO:42), CS02-LC-AA, CS02-HC-AA, CS02-HC-NA (SEQ ID NO:41),CS03-FL-NA (SEQ ID NO:6), CS03-FL-AA, CS03-LC-NA (SEQ ID NO:44),CS03-LC-AA, CS03-HC-AA, CS03-HC-NA (SEQ ID NO:43), CS04-FL-NA (SEQ IDNO:7), CS04-FL-AA, CS04-LC-NA (SEQ ID NO:46), CS04-LC-AA, CS04-HC-AA,CS04-HC-NA, CS05-FL-NA (SEQ ID NO:8), CS05-FL-AA, CS05-LC-NA (SEQ IDNO:48), CS05-LC-AA, CS05-HC-AA, CS05-HC-NA (SEQ ID NO:47), CS06-FL-NA(SEQ ID NO:9), CS06-FL-AA, CS06-LC-NA (SEQ ID NO:50), CS06-LC-AA,CS06-HC-AA, and CS06-HC-NA (SEQ ID NO:49). It should be noted that all“CS” constructs herein encode or contain the FIXp amino acid sequence,although included within the definition of CS constructs are those thatencode or contain the human wild type FIX amino acid sequence.

As used herein, the term “liver-specific expression” refers to thepreferential or predominant in vivo expression of a particular gene(e.g., a codon-altered, transgenic Factor IX gene) in hepatic tissue, ascompared to in other tissues. In some embodiments, liver-specificexpression means that at least 50% of all expression of the particulargene occurs within hepatic tissues of a subject. In other embodiments,liver-specific expression means that at least 55%, 60%, 65%, 70%, 75%,80%, 85%, 90%, 95%, 99%, or 100% of all expression of the particulargene occurs within hepatic tissues of a subject. Accordingly, aliver-specific regulatory element is a regulatory element that drivesliver-specific expression of a gene in hepatic tissue.

As used herein, the terms “less than” X and “less than” X % refer to arange of from 0 to X, exclusive of the value X, e.g., from 0% to X %,exclusive of X %. As used herein, the terms are used interchangeablywith a range starting at 0 or 0% through, but not including, X or X %.

As used herein, the terms “no more than” X or “no more than” X % referto a range of from 0 to X, inclusive of the value X, e.g., from 0% to X%, inclusive of X %. As used herein, the terms are used interchangeablywith a range starting at 0 or 0% through, and including, X or X %.

As used herein, the terms “greater than” X or “greater than” X % referto a range of from X to an upper limit, exclusive of the value X, e.g.,from X % to 100%, exclusive of X %. As used herein, the terms are usedinterchangeably with a range starting at, but not including, X or X %through an upper limit which is 100% in the context of a percentage.

As used herein, the terms “at least” X or “at least” X % refer to arange of from X to an upper limit, inclusive of the value X, e.g., fromX % to 100%, inclusive of X %. As used herein, the terms are usedinterchangeably with a range starting at, and including, X or X %through an upper limit which is 100% in the context of a percentage.

As used herein, the terms “between ‘X’ and ‘Y’,” “between ‘X’% and‘Y’%,” “from ‘X’ to ‘Y’,” and “from ‘X’% to ‘Y’%” refer to a range offrom X to Y, inclusive of the values X and Y, e.g., from X % to Y %,inclusive of X % and Y %. As used herein, the terms are usedinterchangeably with a range starting at X or X % through, andincluding, Y or Y %.

III. Codon-Altered Factor IX Polynucleotides

In some embodiments, the present disclosure provides codon alterednucleic acid compositions encoding Factor IX or a Factor IX variant(with FIXp finding use in particular embodiments). These codon-alteredpolynucleotides provide markedly improved expression of Factor IX whenadministered in an AAV-based gene therapy construct. The codon-alteredpolynucleotides also demonstrate improved AAV-virion packaging, ascompared to conventionally codon-optimized constructs. As demonstratedin Example 1, Applicants have achieve these advantages through thediscovery of several codon-altered polynucleotides (e.g., CS02-FL-NA,CS03-FL-NA, CS04-FL-NA, CS05-FL-NA, and CS06-FL-NA (SEQ ID NOS:5-9respectively)) encoding a Factor IXp polypeptides with a hyperactiveR338L amino acid substitution (based on the mature, single-chain FactorIX polypeptide sequence; R384L based on the Factor IX pre-pro-proteinsequence). As demonstrated in Examples 2 and 3, incorporation of one ormore liver-specific regulatory control element (e.g., CRM8) into genetherapy vectors encoding the Factor IX molecule further increased invivo and in vitro expression of Factor IX and Factor IX activity.

Wild-type Factor IX is encoded with a 28 amino acid signal peptide(FIX-SP-AA (SEQ ID NO:37)) and an 18 amino acid pro-peptide (FIX-PP-AA(SEQ ID NO:38)), which are cleaved from the encoded polypeptide prior toactivation of Factor IXa. As appreciated by those in the art, signalpeptides and/or pro-peptides may be mutated, replaced by signal peptidesand/or pro-peptides from other genes or other organisms, or completelyremoved, without affecting the sequence of the mature polypeptide leftafter the signal and pro-peptide are removed by cellular processing.

Accordingly, in some embodiments, a codon-altered polynucleotide (e.g.,a nucleic acid composition) provided herein has a nucleotide sequencewith high sequence identity to CS02-FL-NA, CS03-FL-NA, CS04-FL-NA,CS05-FL-NA, or CS06-FL-NA (SEQ ID NOS:5-9, respectively) encoding themature Factor IX single-chain polypeptide, that is, the Factor IX lightchain, activation peptide, and heavy chain (e.g., amino acids 47-461 ofthe full-length polypeptide encoded by the wild-type Factor IX gene;FIX-FL-AA (SEQ ID NO:2)).

Additionally, as known in the art, human wild type Factor IX has a 34amino acid activation peptide positioned between the Factor IX lightchain and heavy chain that is excised from the single-chain Factor IXpolypeptide upon activation of the protein. Because the activationpeptide is removed from the active Factor IX polypeptide, the peptideitself is dispensable for ultimate Factor IX activity. Accordingly, itis not required that the Factor IX polypeptides encoded by thecodon-altered polynucleotides disclosed herein have high sequenceidentity to the human wild type activation peptide sequence (FIX-AP-AA(SEQ ID NO:56)). However, the encoded activation peptide should beexcisable upon activation of the Factor IX polypeptide. For example, insome embodiments, the encoded activation peptide should include FactorXI cleavage sites at its N- and C-termini, that are recognizable andcleavable by human Factor IX in-vivo.

Accordingly, in some embodiments, a codon-altered polynucleotide (e.g.,a nucleic acid composition) provided herein encodes for a single-chainFactor IX polypeptide with high sequence identity to the human wild typeFIX light chain sequence (FIX-LC-AA (SEQ ID NO:62)) and human wild typeFIX heavy chain sequence (FIX-HC-AA (SEQ ID NO:63)), and additionallyencode for a polypeptide linker joining the C-terminus of the lightchain to the N-terminus of the heavy chain (e.g., an activation peptide)with two Factor XI cleavage sites.

In some embodiments, the Factor IX light and heavy chains encoded by thecodon-altered polynucleotide are human Factor IX light and heavy chains,respectively, including the FIXp heavy chain. In other embodiments, theFactor IX light and heavy chains encoded by the codon-alteredpolynucleotide are heavy and light chain sequences from another mammal(e.g., porcine Factor IX). In yet other embodiments, the Factor IX lightand heavy chains are chimeric light and heavy chains (e.g., acombination of human and a second mammalian sequence). In yet otherembodiments, the Factor IX light and heavy chains are humanized versionof the light and heavy chains from another mammal, e.g., light and heavychain sequences from another mammal in which human residues aresubstituted at select positions to reduce the immunogenicity of theresulting peptide when administered to a human.

The GC content of human genes varies widely, from less than 25% togreater than 90%. However, in general, human genes with higher GCcontents are expressed at higher levels. For example, Kudla et al. (PLoSBiol., 4(6):80 (2006)) demonstrate that increasing a gene's GC contentincreases expression of the encoded polypeptide, primarily by increasingtranscription and effecting a higher steady state level of the mRNAtranscript. Generally, the desired GC content of a codon-optimized geneconstruct is thought to be equal or greater than 60%. For example, theFactor IX gene in the scAAV8.FIXR338L gene therapy vector wasspecifically codon altered, using the GeneOptimizer software (Geneart),to increase the GC content of the wild type coding sequence from 41% GCto 61% GC. See, Wu Z. et al., Mol Ther 16:280-89 (2008) and Monahan P Eet al., Hum Gene Ther., 26(2):69-81 (2015). However, native AAV genomeshave GC contents of around 56%.

Accordingly, in some embodiments, the codon-altered polynucleotides(e.g., nucleic acid compositions) provided herein have a CG content thatmore closely matches the GC content of native AAV virions (e.g., around56% GC), which is lower than the preferred CG contents ofpolynucleotides that are conventionally codon-optimized for expressionin mammalian cells (e.g., at or above 60% GC). For example, CS02-FL-NA(SEQ ID NO:5) has a GC content of about 54%, CS03-FL-NA (SEQ ID NO:6)has a GC content of about 55%, CS04-FL-NA (SEQ ID NO:7) has a GC contentof about 54.5%, CS05-FL-NA (SEQ ID NO:8) has a GC content of about56.6%, and CS06-FL-NA (SEQ ID NO:9) has a GC content of about 55%. Theseconstructs should provide has improved virion packaging as compared tosimilarly codon-altered sequences with higher GC content.

Thus, in some embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide (e.g., a polynucleotidehaving high sequence identity to one of the CS02-CS06 Factor IX codingsequences) is less than 60%. In some embodiments, the overall GC contentof a codon-altered polynucleotide encoding a Factor IX polypeptide isless than 59%. In some embodiments, the overall GC content of acodon-altered polynucleotide encoding a Factor IX polypeptide is lessthan 58%. In some embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is less than 57%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is no more than 56%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is no more than 55%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is no more than 54%.

In some embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 53% to 59%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 54% to 59%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 55% to 59%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 56% to 59%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 53% to 58%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 54% to 58%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 55% to 58%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 56% to 58%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 53% to 57%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 54% to 57%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 55% to 57%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 56% to 57%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 53% to 56%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 54% to 56%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 55% to 56%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 53% to 55%. Insome embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is from 54% to 55%.

In some embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is 54±0.5%. In someembodiments, the overall GC content of a codon-altered polynucleotideencoding a Factor IX polypeptide is 54±0.4%. In some embodiments, theoverall GC content of a codon-altered polynucleotide encoding a FactorIX polypeptide is 54±0.3%. In some embodiments, the overall GC contentof a codon-altered polynucleotide encoding a Factor IX polypeptide is54±0.2%. In some embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is 54±0.1%. In someembodiments, the overall GC content of a codon-altered polynucleotideencoding a Factor IX polypeptide is 54%.

In some embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is 55±0.5%. In someembodiments, the overall GC content of a codon-altered polynucleotideencoding a Factor IX polypeptide is 55±0.4%. In some embodiments, theoverall GC content of a codon-altered polynucleotide encoding a FactorIX polypeptide is 55±0.3%. In some embodiments, the overall GC contentof a codon-altered polynucleotide encoding a Factor IX polypeptide is55±0.2%. In some embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is 55±0.1%. In someembodiments, the overall GC content of a codon-altered polynucleotideencoding a Factor IX polypeptide is 55%.

In some embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is 56±0.5%. In someembodiments, the overall GC content of a codon-altered polynucleotideencoding a Factor IX polypeptide is 56±0.4%. In some embodiments, theoverall GC content of a codon-altered polynucleotide encoding a FactorIX polypeptide is 56±0.3%. In some embodiments, the overall GC contentof a codon-altered polynucleotide encoding a Factor IX polypeptide is56±0.2%. In some embodiments, the overall GC content of a codon-alteredpolynucleotide encoding a Factor IX polypeptide is 56±0.1%. In someembodiments, the overall GC content of a codon-altered polynucleotideencoding a Factor IX polypeptide is 56%.

It has been theorized that these CpG dinucleotides (i.e., a cytosinenucleotide followed by a guanine nucleotide) induce immune responses viatoll-like receptors, in vivo. Some evidence suggests that CpG-depletedAAV vectors evade immune detection in mice, under certain circumstances(Faust et al., J. Clin. Invest. 2013; 123, 2994-3001). The wild typeFactor IX coding sequence (FIX-FL-NA (SEQ ID NO:1)) contains 20 CpGdinucleotides.

Accordingly, in some embodiments, the nucleic acid compositions (e.g.,codon-altered polynucleotides) provided herein are codon-altered toreduce the number of CpG dinucleotides in the Factor IX coding sequence.For example, CS02-FL-NA (SEQ ID NO:5) has no CpG dinucleotides,CS03-FL-NA (SEQ ID NO:6) has no CpG dinucleotides, CS04-FL-NA (SEQ IDNO:7) has no CpG dinucleotides, CS05-FL-NA (SEQ ID NO:8) has 11 CpGdinucleotides, and CS06-FL-NA (SEQ ID NO:9) has 3 CpG dinucleotides.These constructs should illicit lower immunogenic responses than thewild type Factor IX coding sequence and similarly codon-alteredsequences with higher numbers of CpG dinucleotides.

Thus, in some embodiments, a sequence of a codon-altered polynucleotideencoding a Factor IX polypeptide (e.g., a polynucleotide having highsequence identity to one of the CS02-CS06 Factor IX coding sequences)has less than 20 CpG dinucleotides. In some embodiments, a sequence of acodon-altered polynucleotide encoding a Factor IX polypeptide has lessthan 15 CpG dinucleotides. In some embodiments, a sequence of acodon-altered polynucleotide encoding a Factor IX polypeptide has lessthan 12 CpG dinucleotides. In some embodiments, a sequence of acodon-altered polynucleotide encoding a Factor IX polypeptide has lessthan 10 CpG dinucleotides. In some embodiments, a sequence of acodon-altered polynucleotide encoding a Factor IX polypeptide has lessthan 5 CpG dinucleotides. In some embodiments, a sequence of acodon-altered polynucleotide encoding a Factor IX polypeptide has lessthan 3 CpG dinucleotides. In some embodiments, a sequence of acodon-altered polynucleotide encoding a Factor IX polypeptide has no CpGdinucleotides.

In some embodiments, a sequence of a codon-altered polynucleotideencoding a Factor IX polypeptide has more than 15 CpG dinucleotides. Insome embodiments, a sequence of a codon-altered polynucleotide encodinga Factor IX polypeptide has no more than 12 CpG dinucleotides. In someembodiments, a sequence of a codon-altered polynucleotide encoding aFactor IX polypeptide has no more than 10 CpG dinucleotides. In someembodiments, a sequence of a codon-altered polynucleotide encoding aFactor IX polypeptide has no more than 5 CpG dinucleotides. In someembodiments, a sequence of a codon-altered polynucleotide encoding aFactor IX polypeptide has no more than 3 CpG dinucleotides. In someembodiments, a sequence of a codon-altered polynucleotide encoding aFactor IX polypeptide has no CpG dinucleotides. In some embodiments,sequence of a codon-altered polynucleotide encoding a Factor IXpolypeptide has no more than 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8,7, 6, 5, 4, 3, 2, 1, or no CpG dinucleotides.

A. Factor IX Amino Acid Substitutions

To further increase the efficiency of AAV-vector based expression of theFactor IX constructs described herein, amino acid substitutions know toimprove secretion, increase specific activity, and/or enhanced thestability of Factor IX are further incorporated, in accordance with someimplementations. A number of potential Factor IX variants are known inthe art to increase the plasma levels of FIX activity. These variantsinclude amino acid substitutions that increase Factor IX catalyticactivity (e.g., hyperactive mutants), increase resistance toantithrombin III and/or heparin, increase serum half-life, and result inaltered patterns of post-translational modification.

For example, mutation of residue R338 (PPE) can increase the clottingactivity of Factor IX. For review, see U.S. Pat. No. 6,531,298, thecontents of which are hereby incorporated by reference in its entiretyfor all purposes. As disclosed in U.S. Pat. No. 6,531,298, an arginineto leucine amino acid substitution at this position increases theactivity of Factor IX. This was later confirmed in vivo, where the R338L(PPE) mutation increases Factor IX activity 5-fold to 10-fold in vivo.For review, see Simioni P. et al., N Engl J Med. 361(17):1671-75 (2009),hereby incorporated by reference in its entirety. Accordingly, in someembodiments, the codon-altered polynucleotides described herein encode aFactor IX polypeptide with an amino acid substitution at arginine 384(PPI; residue 338 (PPE). In a specific embodiment, the amino acidsubstitution is R384L (PPI). In other embodiments, the amino acidsubstitution at residue 384 (PPI)/338 (PPE) to a residue other thanleucine. For example, it was reported that an R384A (PPI) amino acidsubstitution provided 2-for to 6-fold higher activity in mice.Schuettrumpf J et al., Blood, 105(6):2316-23 (2005), the content ofwhich is expressly incorporated herein by reference, in its entirety,for all purposes.

Similarly, mutation of residues Y305, K311, S365, and Y391 leads toincreased Factor IX activity on a synthetic substrate. In particular,K311M and K311T single mutations resulted in 2.8-fold and 6.7-foldincreased activity on a synthetic cleavage substrate. Sichler K. et al.,J Biol Chem. 278(6):4121-26 (2003) (using different residue numbering).Further, a Y305F/K311T/Y391T triple mutant resulted in 7000-foldincreased activity on the synthetic substrate. Id. Accordingly, in someembodiments, the codon-altered polynucleotides described herein encode aFactor IX polypeptide with an amino acid substitution at one or more oftyrosine 305 (PPI), lysine 311 (PPI), and tyrosine 391 (PPI). In aspecific embodiment, the amino acid substitution is K311M (PPI). In aspecific embodiment, the amino acid substitution is K311T (PPI). Inanother specific embodiment, the amino acid substitution isY305F/K311T/Y391T (PPI).

Other amino acid substitutions that provide improved properties areknown in the art and may be incorporated into the describedcodon-altered Factor IX polynucleotides. For example, see, U.S. Pat. No.8,778,870, the content of which is expressly incorporated herein byreference, in its entirety, for all purposes.

B. Codon-altered Polynucleotides Encoding a Factor IX Protein

CS02 Codon Altered Polynucleotides

In one embodiment, a nucleic acid composition provided herein includes aFactor IX polynucleotide (e.g., a codon-optimized polynucleotide)encoding a single-chain Factor IX polypeptide, where the Factor IXpolynucleotide includes a nucleotide sequence having high sequenceidentity to CS02-FL-NA (SEQ ID NO:5). In some embodiments, thenucleotide sequence of the Factor IX polynucleotide having high sequenceidentity to CS02-FL-NA (SEQ ID NO:5) has a reduced GC content, ascompared to the wild-type Factor IX coding sequence (FIX-FL-NA (SEQ IDNO:1)). In some embodiments, the nucleotide sequence of the Factor IXpolynucleotide having high sequence identity to CS02-FL-NA (SEQ ID NO:5)has a reduced number of CpG dinucleotides, as compared to the wild-typeFactor IX coding sequence (FIX-FL-NA (SEQ ID NO: 1)).

In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 95% identity to CS02-FL-NA (SEQ ID NO:5). Ina specific embodiment, the sequence of the codon-altered polynucleotidehas at least 96% identity to CS02-FL-NA (SEQ ID NO:5). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 97% identity to CS02-FL-NA (SEQ ID NO:5). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 98% identity to CS02-FL-NA (SEQ ID NO:5). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 99% identity to CS02-FL-NA (SEQ ID NO:5). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 99.5% identity to CS02-FL-NA (SEQ ID NO:5). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 99.9% identity to CS02-FL-NA (SEQ ID NO:5). In another specificembodiment, the sequence of the codon-altered polynucleotide isCS02-FL-NA (SEQ ID NO:5).

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-FL-NA (SEQ ID NO:5) has a GCcontent of less than 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-FL-NA(SEQ ID NO:5) has a GC content of less than 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS02-FL-NA (SEQ ID NO:5) has a GC content of less than 58%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-FL-NA (SEQ ID NO:5) has a GCcontent of less than 57%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-FL-NA(SEQ ID NO:5) has a GC content of less than 56%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS02-FL-NA (SEQ ID NO:5) has a GC content of less than 55%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-FL-NA (SEQ ID NO:5) has a GCcontent of less than 54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-FL-NA (SEQ ID NO:5) has a GCcontent of from 50% to 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-FL-NA(SEQ ID NO:5) has a GC content of from 50% to 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS02-FL-NA (SEQ ID NO:5) has a GC content of from 50% to58%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS02-FL-NA (SEQ ID NO:5)has a GC content of from 50% to 57%. In some embodiments, the sequenceof the codon-altered polynucleotide having high sequence identity toCS02-FL-NA (SEQ ID NO:5) has a GC content of from 50% to 56%. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS02-FL-NA (SEQ ID NO:5) has a GC content offrom 50% to 55%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS02-FL-NA (SEQ ID NO:5)has a GC content of from 50% to 54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-FL-NA (SEQ ID NO:5) has a GCcontent of 53.8%±1.0. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-FL-NA(SEQ ID NO:5) has a GC content of 53.8%±0.8. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS02-FL-NA (SEQ ID NO:5) has a GC content of 53.8%±0.6. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-FL-NA (SEQ ID NO:5) has a GCcontent of 53.8%±0.5. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-FL-NA(SEQ ID NO:5) has a GC content of 53.8%±0.4. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS02-FL-NA (SEQ ID NO:5) has a GC content of 53.8%±0.3. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-FL-NA (SEQ ID NO:5) has a GCcontent of 53.8%±0.2. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-FL-NA(SEQ ID NO:5) has a GC content of 53.8%±0.1. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS02-FL-NA (SEQ ID NO:5) has a GC content of 53.8%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-FL-NA (SEQ ID NO:5) has no morethan 15 CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-FL-NA(SEQ ID NO:5) has no more than 12 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS02-FL-NA (SEQ ID NO:5) has no more than 10CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-FL-NA(SEQ ID NO:5) has no more than 9 CpG dinucleotides. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS02-FL-NA (SEQ ID NO:5) has no more than 8 CpGdinucleotides. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS02-FL-NA (SEQ ID NO:5)has no more than 7 CpG dinucleotides. In some embodiments, the sequenceof the codon-altered polynucleotide having high sequence identity toCS02-FL-NA (SEQ ID NO:5) has no more than 6 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS02-FL-NA (SEQ ID NO:5) has no more than 5CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-FL-NA(SEQ ID NO:5) has no more than 4 CpG dinucleotides. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS02-FL-NA (SEQ ID NO:5) has no more than 3 CpGdinucleotides. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS02-FL-NA (SEQ ID NO:5)has no more than 2 CpG dinucleotides. In some embodiments, the sequenceof the codon-altered polynucleotide having high sequence identity toCS02-FL-NA (SEQ ID NO:5) has no more than 1 CpG dinucleotide. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS02-FL-NA (SEQ ID NO:5) has no CpGdinucleotides.

In some embodiments, the encoded Factor IX polypeptide, e.g., thepolypeptide encoded by the polynucleotide having high sequence homologyto CS02-FL-NA (SEQ ID NO:5), has high sequence identity to the wild typeFactor IX pre-pro-protein sequence FIX-FL-AA (SEQ ID NO:2) and/or thePadua (hFIX(R384L)) pre-pro-protein sequence FIXp-FL-AA (SEQ ID NO:4).The encoded Factor IX polypeptide should retain the ability to becomeactivated into a function Factor IXa protein (e.g., by removal of thesignal peptide and the pro-peptide, and by excision of the activationpolypeptide).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIX-FL-AA (SEQ ID NO:2). In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 90% identityto FIX-FL-AA (SEQ ID NO:2). In one embodiment, the sequence of theencoded Factor IX polypeptide has at least 95% identity to FIX-FL-AA(SEQ ID NO:2). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 96% identity to FIX-FL-AA (SEQ ID NO:2). In oneembodiment, the sequence of the encoded Factor IX polypeptide has atleast 97% identity to FIX-FL-AA (SEQ ID NO:2). In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 98% identityto FIX-FL-AA (SEQ ID NO:2). In one embodiment, the sequence of theencoded Factor IX polypeptide has at least 99% identity to FIX-FL-AA(SEQ ID NO:2). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 99.5% identity to FIX-FL-AA (SEQ ID NO:2). Inone embodiment, the sequence of the encoded Factor IX polypeptide has atleast 99.9% identity to FIX-FL-AA (SEQ ID NO:2). In one embodiment, thesequence of the encoded Factor IX polypeptide is FIX-FL-AA (SEQ IDNO:2).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIXp-FL-AA (SEQ ID NO:4) and includes a leucineat position 384 of the pre-pro-polypeptide (e.g., position 338 of themature Factor IX single-chain polypeptide FIXp-MP-AA (SEQ ID NO: 12)).In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 90% identity to FIXp-FL-AA (SEQ ID NO:4) and includes a leucineat position 384 of the pre-pro-polypeptide. In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 95% identityto FIXp-FL-AA (SEQ ID NO:4) and includes a leucine at position 384 ofthe pre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 96% identity to FIXp-FL-AA (SEQ IDNO:4) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 97% identity FIXp-FL-AA (SEQ ID NO:4) and includes a leucine atposition 384 of the pre-pro-polypeptide. In one embodiment, the sequenceof the encoded Factor IX polypeptide has at least 98% identity toFIXp-FL-AA (SEQ ID NO:4) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 99% identity to FIXp-FL-AA (SEQ IDNO:4) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 99.5% identity to FIXp-FL-AA (SEQ ID NO:4) and includes aleucine at position 384 of the pre-pro-polypeptide. In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 99.9%identity to FIXp-FL-AA (SEQ ID NO:4) and includes a leucine at position384 of the pre-pro-polypeptide. In one embodiment, the sequence of theencoded Factor IX polypeptide is FIXp-FL-AA (SEQ ID NO:4).

In one embodiment, a nucleic acid composition provided herein includes aFactor IX polynucleotide (e.g., a codon-altered polynucleotide) encodinga single-chain Factor IX polypeptide (e.g., having serine proteaseactivity), where the Factor IX polynucleotide includes a nucleotidesequence having high sequence identity to CS02-MP-NA (SEQ ID NO: 13). Insome embodiments, the nucleotide sequence of the Factor IXpolynucleotide having high sequence identity to CS02-MP-NA (SEQ IDNO:13) has a reduced GC content, as compared to the wild-type Factor IXcoding sequence (FIX-FL-NA (SEQ ID NO:1)). In some embodiments, thenucleotide sequence of the Factor IX polynucleotide having high sequenceidentity to CS02-MP-NA (SEQ ID NO: 13) has a reduced number of CpGdinucleotides, as compared to the wild-type Factor IX coding sequence(FIX-FL-NA (SEQ ID NO: 1)).

In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 95% identity to CS02-MP-NA (SEQ ID NO:13).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 96% identity to CS02-MP-NA (SEQ ID NO:13).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 97% identity to CS02-MP-NA (SEQ ID NO: 13).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 98% identity to CS02-MP-NA (SEQ ID NO:13).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 99% identity to CS02-MP-NA (SEQ ID NO:13).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 99.5% identity to CS02-MP-NA (SEQ ID NO:13).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 99.9% identity to CS02-MP-NA (SEQ ID NO:13).In another specific embodiment, the sequence of the codon-alteredpolynucleotide is CS02-MP-NA (SEQ ID NO:13).

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-MP-NA (SEQ ID NO:13) has a GCcontent of less than 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-MP-NA(SEQ ID NO:13) has a GC content of less than 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS02-MP-NA (SEQ ID NO:13) has a GC content of less than 58%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-MP-NA (SEQ ID NO: 13) has a GCcontent of less than 57%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-MP-NA(SEQ ID NO: 13) has a GC content of less than 56%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS02-MP-NA (SEQ ID NO:13) has a GC content of less than 55%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-MP-NA (SEQ ID NO:13) has a GCcontent of less than 54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-MP-NA (SEQ ID NO: 13) has a GCcontent of from 50% to 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-MP-NA(SEQ ID NO:13) has a GC content of from 50% to 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS02-MP-NA (SEQ ID NO: 13) has a GC content of from 50% to58%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS02-MP-NA (SEQ IDNO:13) has a GC content of from 50% to 57%. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS02-MP-NA (SEQ ID NO: 13) has a GC content of from 50% to56%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS02-MP-NA (SEQ ID NO:13) has a GC content of from 50% to 55%. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS02-MP-NA (SEQ ID NO: 13) has a GC content of from 50% to54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-MP-NA (SEQ ID NO:13) has a GCcontent of 53.8%±1.0. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-MP-NA(SEQ ID NO:13) has a GC content of 53.8%±0.8. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS02-MP-NA (SEQ ID NO:13) has a GC content of 53.8%±0.6. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-MP-NA (SEQ ID NO: 13) has a GCcontent of 53.8%±0.5. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-MP-NA(SEQ ID NO: 13) has a GC content of 53.8%±0.4. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS02-MP-NA (SEQ ID NO:13) has a GC content of 53.8%±0.3. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-MP-NA (SEQ ID NO: 13) has a GCcontent of 53.8%±0.2. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-MP-NA(SEQ ID NO:13) has a GC content of 53.8%±0.1. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS02-MP-NA (SEQ ID NO: 13) has a GC content of 53.8%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS02-MP-NA (SEQ ID NO:13) has no morethan 15 CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-MP-NA(SEQ ID NO:13) has no more than 12 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS02-MP-NA (SEQ ID NO:13) has no more than 10CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-MP-NA(SEQ ID NO:13) has no more than 9 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS02-MP-NA (SEQ ID NO: 13) has no more than 8CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-MP-NA(SEQ ID NO: 13) has no more than 7 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS02-MP-NA (SEQ ID NO:13) has no more than 6CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-MP-NA(SEQ ID NO: 13) has no more than 5 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS02-MP-NA (SEQ ID NO:13) has no more than 4CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-MP-NA(SEQ ID NO:13) has no more than 3 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS02-MP-NA (SEQ ID NO:13) has no more than 2CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS02-MP-NA(SEQ ID NO: 13) has no more than 1 CpG dinucleotide. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS02-MP-NA (SEQ ID NO:13) has no CpGdinucleotides.

In some embodiments, the Factor IX polynucleotide high sequence identityto CS02-MP-NA (SEQ ID NO:13) further includes a Factor IX signalpolynucleotide encoding a Factor IX signal peptide having the amino acidsequence of FIX-SP-AA (SEQ ID NO:37). In some embodiments, the Factor IXsignal polynucleotide has a nucleic acid sequence that is at least 90%,95%, 96%, 97%, 98%, 99%, or 100% identical to CS02-SP-NA (SEQ ID NO:25).In some embodiments, the Factor IX signal polynucleotide has a nucleicacid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identical to CS03-SP-NA (SEQ ID NO:26). In some embodiments, the FactorIX signal polynucleotide has a nucleic acid sequence that is at least90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS04-SP-NA (SEQ IDNO:27). In some embodiments, the Factor IX signal polynucleotide has anucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identical to CS05-SP-NA (SEQ ID NO:28). In some embodiments, theFactor IX signal polynucleotide has a nucleic acid sequence that is atleast 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS06-SP-NA (SEQID NO:29).

In some embodiments, the Factor IX polynucleotide high sequence identityto CS02-MP-NA (SEQ ID NO:13) further includes a Factor IX pro-peptidepolynucleotide encoding a Factor IX pro-peptide having the amino acidsequence of FIX-PP-AA (SEQ ID NO:38). In some embodiments, the Factor IXpro-peptide polynucleotide has a nucleic acid sequence that is at least90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS02-PP-NA (SEQ IDNO:31). In some embodiments, the Factor IX pro-peptide polynucleotidehas a nucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%,99%, or 100% identical to CS03-PP-NA (SEQ ID NO:32). In someembodiments, the Factor IX pro-peptide polynucleotide has a nucleic acidsequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identical to CS04-PP-NA (SEQ ID NO:33). In some embodiments, the FactorIX pro-peptide polynucleotide has a nucleic acid sequence that is atleast 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS05-PP-NA (SEQID NO:34). In some embodiments, the Factor IX pro-peptide polynucleotidehas a nucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%,99%, or 100% identical to CS06-PP-NA (SEQ ID NO:35).

In some embodiments, the Factor IX polynucleotide high sequence identityto CS02-MP-NA (SEQ ID NO: 13) further includes a Factor IXpre-pro-peptide polynucleotide encoding a Factor IX pre-pro-peptidehaving the amino acid sequence of FIX-PPP-AA (SEQ ID NO:36). In someembodiments, the Factor IX pre-pro-peptide polynucleotide has a nucleicacid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identical to CS02-PPP-NA (SEQ ID NO:19). In some embodiments, the FactorIX pre-pro-peptide polynucleotide has a nucleic acid sequence that is atleast 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS03-PPP-NA(SEQ ID NO:20). In some embodiments, the Factor IX pre-pro-peptidepolynucleotide has a nucleic acid sequence that is at least 90%, 95%,96%, 97%, 98%, 99%, or 100% identical to CS04-PPP-NA (SEQ ID NO:21). Insome embodiments, the Factor IX pre-pro-peptide polynucleotide has anucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identical to CS05-PPP-NA (SEQ ID NO:22). In some embodiments, theFactor IX pre-pro-peptide polynucleotide has a nucleic acid sequencethat is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical toCS06-PPP-NA (SEQ ID NO:23).

In some embodiments, the encoded Factor IX polypeptide, e.g., thepolypeptide encoded by the polynucleotide having high sequence homologyto CS02-FL-NA (SEQ ID NO:5), has high sequence identity to the wildtype, mature Factor IX single-chain polypeptide sequence FIX-MP-AA (SEQID NO: 10) and/or the mature Padua (hFIX(R384L)) single-chain sequenceFIXp-MP-AA (SEQ ID NO: 12). The encoded Factor IX polypeptide shouldretain the ability to become activated into a function Factor IXaprotein (e.g., by removal of any signal peptide and the pro-peptide, andby excision of the activation polypeptide).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 90%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 95% identity to FIX-MP-AA(SEQ ID NO: 10). In one embodiment, the sequence of the encoded FactorIX polypeptide has at least 96% identity to FIX-MP-AA (SEQ ID NO: 10).In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 97% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 98%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 99% identity to FIX-MP-AA(SEQ ID NO:10). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 99.5% identity to FIX-MP-AA (SEQ ID NO: 10). Inone embodiment, the sequence of the encoded Factor IX polypeptide has atleast 99.9% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide is FIX-MP-AA (SEQ IDNO: 10).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide (e.g., position 338of the mature Factor IX single-chain polypeptide FIXp-MP-AA (SEQ ID NO:12)). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 90% identity to FIXp-MP-AA (SEQ ID NO: 12) andincludes a leucine at position 384 of the pre-pro-polypeptide. In oneembodiment, the sequence of the encoded Factor IX polypeptide has atleast 95% identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucineat position 384 of the pre-pro-polypeptide. In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 96% identityto FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 ofthe pre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 97% identity FIXp-MP-AA (SEQ ID NO:12) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 98% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide. In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 99%identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine atposition 384 of the pre-pro-polypeptide. In one embodiment, the sequenceof the encoded Factor IX polypeptide has at least 99.5% identity toFIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 99.9% identity to FIXp-MP-AA (SEQ IDNO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide is FIXp-MP-AA (SEQ ID NO: 12).

In one embodiment, a codon-altered polynucleotides provided hereinencodes for a single-chain Factor IX polypeptide including a lightchain, a heavy chain, and a polypeptide linker joining the C-terminus ofthe light chain to the N-terminus of the heavy chain. The light chain ofthe Factor IX polypeptide is encoded by a first nucleotide sequencehaving high sequence identity to CS02-LC-NA (SEQ ID NO:42), which is theportion of CS02-FL-NA (SEQ ID NO:5) encoding the Factor IX light chain.The heavy chain of the Factor IX polypeptide is encoded by a secondnucleotide sequence having high sequence identity to CS02-HC-NA (SEQ IDNO:41), which is the portion of CS02-FL-NA (SEQ ID NO:5) encoding theFactor IX heavy chain. The polypeptide linker includes Factor XIcleavage sites, which allow for maturation in vivo (e.g., afterexpression of the precursor single-chain Factor IX polypeptide.

In some embodiments, the first and second nucleotide sequences have atleast 95% sequence identity to CS02-LC-NA and CS02-HC-NA (SEQ ID NOS:42and 41), respectively. In some embodiments, the first and secondnucleotide sequences have at least 96% sequence identity to CS02-LC-NAand CS02-HC-NA (SEQ ID NOS:42 and 41), respectively. In someembodiments, the first and second nucleotide sequences have at least 97%sequence identity to CS02-LC-NA and CS02-HC-NA (SEQ ID NOS:42 and 41),respectively. In some embodiments, the first and second nucleotidesequences have at least 98% sequence identity to CS02-LC-NA andCS02-HC-NA (SEQ ID NOS:42 and 41), respectively. In some embodiments,the first and second nucleotide sequences have at least 99% sequenceidentity to CS02-LC-NA and CS02-HC-NA (SEQ ID NOS:42 and 41),respectively, respectively. In some embodiments, the first and secondnucleotide sequences have at least 99.5% sequence identity to CS02-LC-NAand CS02-HC-NA (SEQ ID NOS:42 and 41), respectively. In someembodiments, the first and second nucleotide sequences have at least99.9% sequence identity to CS02-LC-NA and CS02-HC-NA (SEQ ID NOS:42 and41), respectively. In some embodiments, the first and second nucleotidesequences are CS02-LC-NA and CS02-HC-NA (SEQ ID NOS:42 and 41),respectively.

In some embodiments, the polypeptide linker of the Factor IX constructis encoded by a third nucleotide sequence having high sequence identityto CS02-AP-NA (SEQ ID NO:57), which is a codon-altered sequence encodingthe wild type Factor IX activation polypeptide, e.g., amino acids192-226 of FIX-FL-AA (SEQ ID NO:2). In some embodiments, the thirdnucleotide sequence has at least 80% identity to CS02-AP-NA (SEQ IDNO:57). In some embodiments, the third nucleotide sequence has at least90% identity to CS02-AP-NA (SEQ ID NO:57). In some embodiments, thethird nucleotide sequence has at least 95% identity to CS02-AP-NA (SEQID NO:57). In some embodiments, the third nucleotide sequence has atleast 96% identity to CS02-AP-NA (SEQ ID NO:57). In some embodiments,the third nucleotide sequence has at least 97% identity to CS02-AP-NA(SEQ ID NO:57). In some embodiments, the third nucleotide sequence hasat least 98% identity to CS02-AP-NA (SEQ ID NO:57). In some embodiments,the third nucleotide sequence has at least 99% identity to CS02-AP-NA(SEQ ID NO:57). In some embodiments, the third nucleotide sequence isCS02-AP-NA (SEQ ID NO:57).

In some embodiments, the encoded Factor IX polypeptide also includes asignal peptide (e.g., a Factor IX signal peptide) and/or a pro-peptide(e.g., a Factor IX pro-peptide). In some embodiments, the signal peptideis the wild-type Factor IX signal peptide (FIX-SP-AA (SEQ ID NO:37)). Insome embodiments, the signal peptide is encoded by a codon-alteredpolynucleotide sequence having high sequence identity (e.g., at least95%, 96%, 97%, 98%, or 99%) to CS02-SP-NA (SEQ ID NO:25). In someembodiments, the pro-peptide is the wild-type Factor IX pro-peptide(FIX-PP-AA (SEQ ID NO:38)). In some embodiments, the pro-peptide peptideis encoded by a codon-altered polynucleotide sequence having highsequence identity (e.g., at least 95%, 96%, 97%, 98%, or 99%) toCS02-PP-NA (SEQ ID NO:31).

In some embodiments, the encoded Factor IX polypeptide, e.g., thepolypeptide encoded by the polynucleotide having high sequence homologyto CS02-LC-NA (SEQ ID NO:42) and CS02-HC-NA (SEQ ID NO:41), has highsequence identity to the wild type, mature Factor IX single-chainpolypeptide sequence FIX-MP-AA (SEQ ID NO:10) and/or the mature Padua(hFIX(R384L)) single-chain sequence FIXp-MP-AA (SEQ ID NO: 12). Theencoded Factor IX polypeptide should retain the ability to becomeactivated into a function Factor IXa protein (e.g., by removal of anysignal peptide and the pro-peptide, and by excision of the activationpolypeptide).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 90%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 95% identity to FIX-MP-AA(SEQ ID NO: 10). In one embodiment, the sequence of the encoded FactorIX polypeptide has at least 96% identity to FIX-MP-AA (SEQ ID NO: 10).In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 97% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 98%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 99% identity to FIX-MP-AA(SEQ ID NO:10). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 99.5% identity to FIX-MP-AA (SEQ ID NO: 10). Inone embodiment, the sequence of the encoded Factor IX polypeptide has atleast 99.9% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide is FIX-MP-AA (SEQ IDNO: 10).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide (e.g., position 338of the mature Factor IX single-chain polypeptide FIXp-MP-AA (SEQ ID NO:12)). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 90% identity to FIXp-MP-AA (SEQ ID NO: 12) andincludes a leucine at position 384 of the pre-pro-polypeptide. In oneembodiment, the sequence of the encoded Factor IX polypeptide has atleast 95% identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucineat position 384 of the pre-pro-polypeptide. In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 96% identityto FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 ofthe pre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 97% identity FIXp-MP-AA (SEQ ID NO:12) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 98% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide. In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 99%identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine atposition 384 of the pre-pro-polypeptide. In one embodiment, the sequenceof the encoded Factor IX polypeptide has at least 99.5% identity toFIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 99.9% identity to FIXp-MP-AA (SEQ IDNO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide is FIXp-MP-AA (SEQ ID NO: 12).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a self-complementarypolynucleotide of structure A, where the FIX coding sequence portion ofthe polynucleotide includes a nucleic acid sequence, encoding a matureFactor IX polypeptide, that has at least 95%, 96%, 97%, 98%, 99%, 99.5%,99.9%, or 100% identity to CS02-MP-NA (SEQ ID NO: 13). In someembodiments, the FIX coding sequence portion of the polynucleotide alsoincludes a nucleic acid sequence, encoding a Factor IX signal peptide,that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to oneof FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25), CS03-SP-NA (SEQID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ ID NO:28), andCS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIX coding sequenceportion of the polynucleotide also includes a nucleic acid sequence,encoding a Factor IX pro-peptide (optionally in combination with anucleic acid sequence for a Factor IX signal peptide, as describedabove), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identityto one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ ID NO:31),CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA (SEQ IDNO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, the FIXcoding sequence portion of the polynucleotide includes a nucleic acidsequence, encoding a pre-pro-Factor IX polypeptide, that has at least95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity to CS02-FL-NA(SEQ ID NO:5).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a self-complementarypolynucleotide of structure B, where the FIX coding sequence portion ofthe polynucleotide includes a nucleic acid sequence, encoding a matureFactor IX polypeptide, that has at least 95%, 96%, 97%, 98%, 99%, 99.5%,99.9%, or 100% identity to CS02-MP-NA (SEQ ID NO: 13). In someembodiments, the FIX coding sequence portion of the polynucleotide alsoincludes a nucleic acid sequence, encoding a Factor IX signal peptide,that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to oneof FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25), CS03-SP-NA (SEQID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ ID NO:28), andCS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIX coding sequenceportion of the polynucleotide also includes a nucleic acid sequence,encoding a Factor IX pro-peptide (optionally in combination with anucleic acid sequence for a Factor IX signal peptide, as describedabove), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identityto one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ ID NO:31),CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA (SEQ IDNO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, the FIXcoding sequence portion of the polynucleotide includes a nucleic acidsequence, encoding a pre-pro-Factor IX polypeptide, that has at least95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity to CS02-FL-NA(SEQ ID NO:5).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a polynucleotide of structure C(e.g., a single-stranded polynucleotide), where the FIX coding sequenceportion of the polynucleotide includes a nucleic acid sequence, encodinga mature Factor IX polypeptide, that has at least 95%, 96%, 97%, 98%,99%, 99.5%, 99.9%, or 100% identity to CS02-MP-NA (SEQ ID NO:13). Insome embodiments, the FIX coding sequence portion of the polynucleotidealso includes a nucleic acid sequence, encoding a Factor IX signalpeptide, that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identity to one of FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25),CS03-SP-NA (SEQ ID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ IDNO:28), and CS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIXcoding sequence portion of the polynucleotide also includes a nucleicacid sequence, encoding a Factor IX pro-peptide (optionally incombination with a nucleic acid sequence for a Factor IX signal peptide,as described above), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identity to one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ IDNO:31), CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA(SEQ ID NO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, theFIX coding sequence portion of the polynucleotide includes a nucleicacid sequence, encoding a pre-pro-Factor IX polypeptide, that has atleast 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity toCS02-FL-NA (SEQ ID NO:5).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a polynucleotide of structure D(e.g., a single-stranded polynucleotide), where the FIX coding sequenceportion of the polynucleotide includes a nucleic acid sequence, encodinga mature Factor IX polypeptide, that has at least 95%, 96%, 97%, 98%,99%, 99.5%, 99.9%, or 100% identity to CS02-MP-NA (SEQ ID NO:13). Insome embodiments, the FIX coding sequence portion of the polynucleotidealso includes a nucleic acid sequence, encoding a Factor IX signalpeptide, that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identity to one of FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25),CS03-SP-NA (SEQ ID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ IDNO:28), and CS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIXcoding sequence portion of the polynucleotide also includes a nucleicacid sequence, encoding a Factor IX pro-peptide (optionally incombination with a nucleic acid sequence for a Factor IX signal peptide,as described above), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identity to one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ IDNO:31), CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA(SEQ ID NO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, theFIX coding sequence portion of the polynucleotide includes a nucleicacid sequence, encoding a pre-pro-Factor IX polypeptide, that has atleast 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity toCS02-FL-NA (SEQ ID NO:5).

CS03 Codon Altered Polynucleotides

In one embodiment, a nucleic acid composition provided herein includes aFactor IX polynucleotide (e.g., a codon-altered polynucleotide) encodinga single-chain Factor IX polypeptide, where the Factor IX polynucleotideincludes a nucleotide sequence having high sequence identity toCS03-FL-NA (SEQ ID NO:6). In some embodiments, the nucleotide sequenceof the Factor IX polynucleotide having high sequence identity toCS03-FL-NA (SEQ ID NO:6) has a reduced GC content, as compared to thewild-type Factor IX coding sequence (FIX-FL-NA (SEQ ID NO:1)). In someembodiments, the nucleotide sequence of the Factor IX polynucleotidehaving high sequence identity to CS03-FL-NA (SEQ ID NO:6) has a reducednumber of CpG dinucleotides, as compared to the wild-type Factor IXcoding sequence (FIX-FL-NA (SEQ ID NO: 1)).

In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 95% identity to CS03-FL-NA (SEQ ID NO:6). Ina specific embodiment, the sequence of the codon-altered polynucleotidehas at least 96% identity to CS03-FL-NA (SEQ ID NO:6). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 97% identity to CS03-FL-NA (SEQ ID NO:6). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 98% identity to CS03-FL-NA (SEQ ID NO:6). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 99% identity to CS03-FL-NA (SEQ ID NO:6). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 99.5% identity to CS03-FL-NA (SEQ ID NO:6). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 99.9% identity to CS03-FL-NA (SEQ ID NO:6). In another specificembodiment, the sequence of the codon-altered polynucleotide isCS03-FL-NA (SEQ ID NO:6).

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-FL-NA (SEQ ID NO:6) has a GCcontent of less than 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-FL-NA(SEQ ID NO:6) has a GC content of less than 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS03-FL-NA (SEQ ID NO:6) has a GC content of less than 58%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-FL-NA (SEQ ID NO:6) has a GCcontent of less than 57%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-FL-NA(SEQ ID NO:6) has a GC content of less than 56%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS03-FL-NA (SEQ ID NO:6) has a GC content of less than 55%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-FL-NA (SEQ ID NO:6) has a GCcontent of less than 54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-FL-NA (SEQ ID NO:6) has a GCcontent of from 50% to 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-FL-NA(SEQ ID NO:6) has a GC content of from 50% to 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS03-FL-NA (SEQ ID NO:6) has a GC content of from 50% to58%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS03-FL-NA (SEQ ID NO:6)has a GC content of from 50% to 57%. In some embodiments, the sequenceof the codon-altered polynucleotide having high sequence identity toCS03-FL-NA (SEQ ID NO:6) has a GC content of from 50% to 56%. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS03-FL-NA (SEQ ID NO:6) has a GC content offrom 50% to 55%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS03-FL-NA (SEQ ID NO:6)has a GC content of from 50% to 54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-FL-NA (SEQ ID NO:6) has a GCcontent of 53.8%±1.0. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-FL-NA(SEQ ID NO:6) has a GC content of 53.8%±0.8. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS03-FL-NA (SEQ ID NO:6) has a GC content of 53.8%±0.6. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-FL-NA (SEQ ID NO:6) has a GCcontent of 53.8%±0.5. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-FL-NA(SEQ ID NO:6) has a GC content of 53.8%±0.4. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS03-FL-NA (SEQ ID NO:6) has a GC content of 53.8%±0.3. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-FL-NA (SEQ ID NO:6) has a GCcontent of 53.8%±0.2. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-FL-NA(SEQ ID NO:6) has a GC content of 53.8%±0.1. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS03-FL-NA (SEQ ID NO:6) has a GC content of 53.8%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-FL-NA (SEQ ID NO:6) has no morethan 15 CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-FL-NA(SEQ ID NO:6) has no more than 12 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS03-FL-NA (SEQ ID NO:6) has no more than 10CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-FL-NA(SEQ ID NO:6) has no more than 9 CpG dinucleotides. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS03-FL-NA (SEQ ID NO:6) has no more than 8 CpGdinucleotides. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS03-FL-NA (SEQ ID NO:6)has no more than 7 CpG dinucleotides. In some embodiments, the sequenceof the codon-altered polynucleotide having high sequence identity toCS03-FL-NA (SEQ ID NO:6) has no more than 6 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS03-FL-NA (SEQ ID NO:6) has no more than 5CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-FL-NA(SEQ ID NO:6) has no more than 4 CpG dinucleotides. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS03-FL-NA (SEQ ID NO:6) has no more than 3 CpGdinucleotides. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS03-FL-NA (SEQ ID NO:6)has no more than 2 CpG dinucleotides. In some embodiments, the sequenceof the codon-altered polynucleotide having high sequence identity toCS03-FL-NA (SEQ ID NO:6) has no more than 1 CpG dinucleotide. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS03-FL-NA (SEQ ID NO:6) has no CpGdinucleotides.

In some embodiments, the encoded Factor IX polypeptide, e.g., thepolypeptide encoded by the polynucleotide having high sequence homologyto CS03-FL-NA (SEQ ID NO:6), has high sequence identity to the wild typeFactor IX pre-pro-protein sequence FIX-FL-AA (SEQ ID NO:2) and/or thePadua (hFIX(R384L)) pre-pro-protein sequence FIXp-FL-AA (SEQ ID NO:4).The encoded Factor IX polypeptide should retain the ability to becomeactivated into a function Factor IXa protein (e.g., by removal of thesignal peptide and the pro-peptide, and by excision of the activationpolypeptide).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIX-FL-AA (SEQ ID NO:2). In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 90% identityto FIX-FL-AA (SEQ ID NO:2). In one embodiment, the sequence of theencoded Factor IX polypeptide has at least 95% identity to FIX-FL-AA(SEQ ID NO:2). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 96% identity to FIX-FL-AA (SEQ ID NO:2). In oneembodiment, the sequence of the encoded Factor IX polypeptide has atleast 97% identity to FIX-FL-AA (SEQ ID NO:2). In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 98% identityto FIX-FL-AA (SEQ ID NO:2). In one embodiment, the sequence of theencoded Factor IX polypeptide has at least 99% identity to FIX-FL-AA(SEQ ID NO:2). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 99.5% identity to FIX-FL-AA (SEQ ID NO:2). Inone embodiment, the sequence of the encoded Factor IX polypeptide has atleast 99.9% identity to FIX-FL-AA (SEQ ID NO:2). In one embodiment, thesequence of the encoded Factor IX polypeptide is FIX-FL-AA (SEQ IDNO:2).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIXp-FL-AA (SEQ ID NO:4) and includes a leucineat position 384 of the pre-pro-polypeptide (e.g., position 338 of themature Factor IX single-chain polypeptide FIXp-MP-AA (SEQ ID NO: 12)).In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 90% identity to FIXp-FL-AA (SEQ ID NO:4) and includes a leucineat position 384 of the pre-pro-polypeptide. In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 95% identityto FIXp-FL-AA (SEQ ID NO:4) and includes a leucine at position 384 ofthe pre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 96% identity to FIXp-FL-AA (SEQ IDNO:4) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 97% identity FIXp-FL-AA (SEQ ID NO:4) and includes a leucine atposition 384 of the pre-pro-polypeptide. In one embodiment, the sequenceof the encoded Factor IX polypeptide has at least 98% identity toFIXp-FL-AA (SEQ ID NO:4) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 99% identity to FIXp-FL-AA (SEQ IDNO:4) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 99.5% identity to FIXp-FL-AA (SEQ ID NO:4) and includes aleucine at position 384 of the pre-pro-polypeptide. In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 99.9%identity to FIXp-FL-AA (SEQ ID NO:4) and includes a leucine at position384 of the pre-pro-polypeptide. In one embodiment, the sequence of theencoded Factor IX polypeptide is FIXp-FL-AA (SEQ ID NO:4).

In one embodiment, a nucleic acid composition provided herein includes aFactor IX polynucleotide (e.g., a codon-altered polynucleotide) encodinga single-chain Factor IX polypeptide (e.g., having serine proteaseactivity), where the Factor IX polynucleotide includes a nucleotidesequence having high sequence identity to CS03-MP-NA (SEQ ID NO: 14). Insome embodiments, the nucleotide sequence of the Factor IXpolynucleotide having high sequence identity to CS03-MP-NA (SEQ ID NO:14) has a reduced GC content, as compared to the wild-type Factor IXcoding sequence (FIX-FL-NA (SEQ ID NO:1)). In some embodiments, thenucleotide sequence of the Factor IX polynucleotide having high sequenceidentity to CS03-MP-NA (SEQ ID NO: 14) has a reduced number of CpGdinucleotides, as compared to the wild-type Factor IX coding sequence(FIX-FL-NA (SEQ ID NO: 1)).

In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 95% identity to CS03-MP-NA (SEQ ID NO: 14).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 96% identity to CS03-MP-NA (SEQ ID NO:14).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 97% identity to CS03-MP-NA (SEQ ID NO: 14).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 98% identity to CS03-MP-NA (SEQ ID NO:14).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 99% identity to CS03-MP-NA (SEQ ID NO:14).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 99.5% identity to CS03-MP-NA (SEQ ID NO:14).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 99.9% identity to CS03-MP-NA (SEQ ID NO:14). In another specific embodiment, the sequence of the codon-alteredpolynucleotide is CS03-MP-NA (SEQ ID NO: 14).

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-MP-NA (SEQ ID NO:14) has a GCcontent of less than 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-MP-NA(SEQ ID NO: 14) has a GC content of less than 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS03-MP-NA (SEQ ID NO:14) has a GC content of less than 58%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-MP-NA (SEQ ID NO: 14) has a GCcontent of less than 57%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-MP-NA(SEQ ID NO: 14) has a GC content of less than 56%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS03-MP-NA (SEQ ID NO:14) has a GC content of less than 55%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-MP-NA (SEQ ID NO:14) has a GCcontent of less than 54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-MP-NA (SEQ ID NO: 14) has a GCcontent of from 50% to 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-MP-NA(SEQ ID NO:14) has a GC content of from 50% to 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS03-MP-NA (SEQ ID NO:14) has a GC content of from 50% to58%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS03-MP-NA (SEQ ID NO:14) has a GC content of from 50% to 57%. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS03-MP-NA (SEQ ID NO: 14) has a GC content of from 50% to56%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS03-MP-NA (SEQ ID NO:14) has a GC content of from 50% to 55%. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS03-MP-NA (SEQ ID NO: 14) has a GC content of from 50% to54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-MP-NA (SEQ ID NO:14) has a GCcontent of 53.8%±1.0. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-MP-NA(SEQ ID NO:14) has a GC content of 53.8%±0.8. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS03-MP-NA (SEQ ID NO:14) has a GC content of 53.8%±0.6. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-MP-NA (SEQ ID NO: 14) has a GCcontent of 53.8%±0.5. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-MP-NA(SEQ ID NO: 14) has a GC content of 53.8%±0.4. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS03-MP-NA (SEQ ID NO:14) has a GC content of 53.8%±0.3. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-MP-NA (SEQ ID NO: 14) has a GCcontent of 53.8%±0.2. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-MP-NA(SEQ ID NO:14) has a GC content of 53.8%±0.1. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS03-MP-NA (SEQ ID NO: 14) has a GC content of 53.8%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS03-MP-NA (SEQ ID NO:14) has no morethan 15 CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-MP-NA(SEQ ID NO:14) has no more than 12 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS03-MP-NA (SEQ ID NO:14) has no more than 10CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-MP-NA(SEQ ID NO: 14) has no more than 9 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS03-MP-NA (SEQ ID NO: 14) has no more than 8CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-MP-NA(SEQ ID NO: 14) has no more than 7 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS03-MP-NA (SEQ ID NO:14) has no more than 6CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-MP-NA(SEQ ID NO: 14) has no more than 5 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS03-MP-NA (SEQ ID NO:14) has no more than 4CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-MP-NA(SEQ ID NO: 14) has no more than 3 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS03-MP-NA (SEQ ID NO: 14) has no more than 2CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS03-MP-NA(SEQ ID NO: 14) has no more than 1 CpG dinucleotide. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS03-MP-NA (SEQ ID NO:14) has no CpGdinucleotides.

In some embodiments, the Factor IX polynucleotide high sequence identityto CS03-MP-NA (SEQ ID NO:14) further includes a Factor IX signalpolynucleotide encoding a Factor IX signal peptide having the amino acidsequence of FIX-SP-AA (SEQ ID NO:37). In some embodiments, the Factor IXsignal polynucleotide has a nucleic acid sequence that is at least 90%,95%, 96%, 97%, 98%, 99%, or 100% identical to CS02-SP-NA (SEQ ID NO:25).In some embodiments, the Factor IX signal polynucleotide has a nucleicacid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identical to CS03-SP-NA (SEQ ID NO:26). In some embodiments, the FactorIX signal polynucleotide has a nucleic acid sequence that is at least90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS04-SP-NA (SEQ IDNO:27). In some embodiments, the Factor IX signal polynucleotide has anucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identical to CS05-SP-NA (SEQ ID NO:28). In some embodiments, theFactor IX signal polynucleotide has a nucleic acid sequence that is atleast 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS06-SP-NA (SEQID NO:29).

In some embodiments, the Factor IX polynucleotide high sequence identityto CS03-MP-NA (SEQ ID NO:14) further includes a Factor IX pro-peptidepolynucleotide encoding a Factor IX pro-peptide having the amino acidsequence of FIX-PP-AA (SEQ ID NO:38). In some embodiments, the Factor IXpro-peptide polynucleotide has a nucleic acid sequence that is at least90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS02-PP-NA (SEQ IDNO:31). In some embodiments, the Factor IX pro-peptide polynucleotidehas a nucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%,99%, or 100% identical to CS03-PP-NA (SEQ ID NO:32). In someembodiments, the Factor IX pro-peptide polynucleotide has a nucleic acidsequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identical to CS04-PP-NA (SEQ ID NO:33). In some embodiments, the FactorIX pro-peptide polynucleotide has a nucleic acid sequence that is atleast 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS05-PP-NA (SEQID NO:34). In some embodiments, the Factor IX pro-peptide polynucleotidehas a nucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%,99%, or 100% identical to CS06-PP-NA (SEQ ID NO:35).

In some embodiments, the Factor IX polynucleotide high sequence identityto CS03-MP-NA (SEQ ID NO: 14) further includes a Factor IXpre-pro-peptide polynucleotide encoding a Factor IX pre-pro-peptidehaving the amino acid sequence of FIX-PPP-AA (SEQ ID NO:36). In someembodiments, the Factor IX pre-pro-peptide polynucleotide has a nucleicacid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identical to CS02-PPP-NA (SEQ ID NO:19). In some embodiments, the FactorIX pre-pro-peptide polynucleotide has a nucleic acid sequence that is atleast 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS03-PPP-NA(SEQ ID NO:20). In some embodiments, the Factor IX pre-pro-peptidepolynucleotide has a nucleic acid sequence that is at least 90%, 95%,96%, 97%, 98%, 99%, or 100% identical to CS04-PPP-NA (SEQ ID NO:21). Insome embodiments, the Factor IX pre-pro-peptide polynucleotide has anucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identical to CS05-PPP-NA (SEQ ID NO:22). In some embodiments, theFactor IX pre-pro-peptide polynucleotide has a nucleic acid sequencethat is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical toCS06-PPP-NA (SEQ ID NO:23).

In some embodiments, the encoded Factor IX polypeptide, e.g., thepolypeptide encoded by the polynucleotide having high sequence homologyto CS03-FL-NA (SEQ ID NO:6), has high sequence identity to the wildtype, mature Factor IX single-chain polypeptide sequence FIX-MP-AA (SEQID NO: 10) and/or the mature Padua (hFIX(R384L)) single-chain sequenceFIXp-MP-AA (SEQ ID NO: 12). The encoded Factor IX polypeptide shouldretain the ability to become activated into a function Factor IXaprotein (e.g., by removal of any signal peptide and the pro-peptide, andby excision of the activation polypeptide).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 90%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 95% identity to FIX-MP-AA(SEQ ID NO: 10). In one embodiment, the sequence of the encoded FactorIX polypeptide has at least 96% identity to FIX-MP-AA (SEQ ID NO: 10).In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 97% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 98%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 99% identity to FIX-MP-AA(SEQ ID NO:10). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 99.5% identity to FIX-MP-AA (SEQ ID NO: 10). Inone embodiment, the sequence of the encoded Factor IX polypeptide has atleast 99.9% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide is FIX-MP-AA (SEQ IDNO: 10).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide (e.g., position 338of the mature Factor IX single-chain polypeptide FIXp-MP-AA (SEQ ID NO:12)). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 90% identity to FIXp-MP-AA (SEQ ID NO: 12) andincludes a leucine at position 384 of the pre-pro-polypeptide. In oneembodiment, the sequence of the encoded Factor IX polypeptide has atleast 95% identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucineat position 384 of the pre-pro-polypeptide. In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 96% identityto FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 ofthe pre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 97% identity FIXp-MP-AA (SEQ ID NO:12) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 98% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide. In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 99%identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine atposition 384 of the pre-pro-polypeptide. In one embodiment, the sequenceof the encoded Factor IX polypeptide has at least 99.5% identity toFIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 99.9% identity to FIXp-MP-AA (SEQ IDNO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide is FIXp-MP-AA (SEQ ID NO: 12).

In one embodiment, a codon-altered polynucleotides provided hereinencodes for a single-chain Factor IX polypeptide including a lightchain, a heavy chain, and a polypeptide linker joining the C-terminus ofthe light chain to the N-terminus of the heavy chain. The light chain ofthe Factor IX polypeptide is encoded by a first nucleotide sequencehaving high sequence identity to CS03-LC-NA (SEQ ID NO:44), which is theportion of CS03-FL-NA (SEQ ID NO:6) encoding the Factor IX light chain.The heavy chain of the Factor IX polypeptide is encoded by a secondnucleotide sequence having high sequence identity to CS03-HC-NA (SEQ IDNO:43), which is the portion of CS03-FL-NA (SEQ ID NO:6) encoding theFactor IX heavy chain. The polypeptide linker includes Factor XIcleavage sites, which allow for maturation in vivo (e.g., afterexpression of the precursor single-chain Factor IX polypeptide.

In some embodiments, the first and second nucleotide sequences have atleast 95% sequence identity to CS03-LC-NA (SEQ ID NO:44) and CS03-HC-NA(SEQ ID NO:43), respectively. In some embodiments, the first and secondnucleotide sequences have at least 96% sequence identity to CS03-LC-NA(SEQ ID NO:44) and CS03-HC-NA (SEQ ID NO:43), respectively. In someembodiments, the first and second nucleotide sequences have at least 97%sequence identity to CS03-LC-NA (SEQ ID NO:44) and CS03-HC-NA (SEQ IDNO:43), respectively. In some embodiments, the first and secondnucleotide sequences have at least 98% sequence identity to CS03-LC-NA(SEQ ID NO:44) and CS03-HC-NA (SEQ ID NO:43), respectively. In someembodiments, the first and second nucleotide sequences have at least 99%sequence identity to CS03-LC-NA (SEQ ID NO:44) and CS03-HC-NA (SEQ IDNO:43), respectively, respectively. In some embodiments, the first andsecond nucleotide sequences have at least 99.5% sequence identity toCS03-LC-NA (SEQ ID NO:44) and CS03-HC-NA (SEQ ID NO:43), respectively.In some embodiments, the first and second nucleotide sequences have atleast 99.9% sequence identity to CS03-LC-NA (SEQ ID NO:44) andCS03-HC-NA (SEQ ID NO:43), respectively. In some embodiments, the firstand second nucleotide sequences are CS03-LC-NA (SEQ ID NO:44) andCS03-HC-NA (SEQ ID NO:43), respectively.

In some embodiments, the polypeptide linker of the Factor IX constructis encoded by a third nucleotide sequence having high sequence identityto CS03-AP-NA (SEQ ID NO:58), which is a codon-altered sequence encodingthe wild type Factor IX activation polypeptide, e.g., amino acids192-226 of FIX-FL-AA (SEQ ID NO:2). In some embodiments, the thirdnucleotide sequence has at least 80% identity to CS03-AP-NA (SEQ IDNO:58). In some embodiments, the third nucleotide sequence has at least90% identity to CS03-AP-NA (SEQ ID NO:58). In some embodiments, thethird nucleotide sequence has at least 95% identity to CS03-AP-NA (SEQID NO:58). In some embodiments, the third nucleotide sequence has atleast 96% identity to CS03-AP-NA (SEQ ID NO:58). In some embodiments,the third nucleotide sequence has at least 97% identity to CS03-AP-NA(SEQ ID NO:58). In some embodiments, the third nucleotide sequence hasat least 98% identity to CS03-AP-NA (SEQ ID NO:58). In some embodiments,the third nucleotide sequence has at least 99% identity to CS03-AP-NA(SEQ ID NO:58). In some embodiments, the third nucleotide sequence isCS03-AP-NA (SEQ ID NO:58).

In some embodiments, the encoded Factor IX polypeptide also includes asignal peptide (e.g., a Factor IX signal peptide) and/or a pro-peptide(e.g., a Factor IX pro-peptide). In some embodiments, the signal peptideis the wild-type Factor IX signal peptide (FIX-SP-AA (SEQ ID NO:37)). Insome embodiments, the signal peptide is encoded by a codon-alteredpolynucleotide sequence having high sequence identity (e.g., at least95%, 96%, 97%, 98%, or 99%) to CS03-SP-NA (SEQ ID NO:26). In someembodiments, the pro-peptide is the wild-type Factor IX pro-peptide(FIX-PP-AA (SEQ ID NO:38)). In some embodiments, the pro-peptide peptideis encoded by a codon-altered polynucleotide sequence having highsequence identity (e.g., at least 95%, 96%, 97%, 98%, or 99%) toCS03-PP-NA (SEQ ID NO:32).

In some embodiments, the encoded Factor IX polypeptide, e.g., thepolypeptide encoded by the polynucleotide having high sequence homologyto CS03-LC-NA (SEQ ID NO:44) and CS03-HC-NA (SEQ ID NO:43), has highsequence identity to the wild type, mature Factor IX single-chainpolypeptide sequence FIX-MP-AA (SEQ ID NO:10) and/or the mature Padua(hFIX(R384L)) single-chain sequence FIXp-MP-AA (SEQ ID NO: 12). Theencoded Factor IX polypeptide should retain the ability to becomeactivated into a function Factor IXa protein (e.g., by removal of anysignal peptide and the pro-peptide, and by excision of the activationpolypeptide).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 90%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 95% identity to FIX-MP-AA(SEQ ID NO: 10). In one embodiment, the sequence of the encoded FactorIX polypeptide has at least 96% identity to FIX-MP-AA (SEQ ID NO: 10).In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 97% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 98%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 99% identity to FIX-MP-AA(SEQ ID NO:10). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 99.5% identity to FIX-MP-AA (SEQ ID NO: 10). Inone embodiment, the sequence of the encoded Factor IX polypeptide has atleast 99.9% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide is FIX-MP-AA (SEQ IDNO: 10).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide (e.g., position 338of the mature Factor IX single-chain polypeptide FIXp-MP-AA (SEQ ID NO:12)). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 90% identity to FIXp-MP-AA (SEQ ID NO: 12) andincludes a leucine at position 384 of the pre-pro-polypeptide. In oneembodiment, the sequence of the encoded Factor IX polypeptide has atleast 95% identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucineat position 384 of the pre-pro-polypeptide. In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 96% identityto FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 ofthe pre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 97% identity FIXp-MP-AA (SEQ ID NO:12) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 98% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide. In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 99%identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine atposition 384 of the pre-pro-polypeptide. In one embodiment, the sequenceof the encoded Factor IX polypeptide has at least 99.5% identity toFIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 99.9% identity to FIXp-MP-AA (SEQ IDNO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide is FIXp-MP-AA (SEQ ID NO: 12).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a self-complementarypolynucleotide of structure A, where the FIX coding sequence portion ofthe polynucleotide includes a nucleic acid sequence, encoding a matureFactor IX polypeptide, that has at least 95%, 96%, 97%, 98%, 99%, 99.5%,99.9%, or 100% identity to CS03-MP-NA (SEQ ID NO: 14). In someembodiments, the FIX coding sequence portion of the polynucleotide alsoincludes a nucleic acid sequence, encoding a Factor IX signal peptide,that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to oneof FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25), CS03-SP-NA (SEQID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ ID NO:28), andCS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIX coding sequenceportion of the polynucleotide also includes a nucleic acid sequence,encoding a Factor IX pro-peptide (optionally in combination with anucleic acid sequence for a Factor IX signal peptide, as describedabove), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identityto one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ ID NO:31),CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA (SEQ IDNO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, the FIXcoding sequence portion of the polynucleotide includes a nucleic acidsequence, encoding a pre-pro-Factor IX polypeptide, that has at least95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity to CS03-FL-NA(SEQ ID NO:6).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a self-complementarypolynucleotide of structure B, where the FIX coding sequence portion ofthe polynucleotide includes a nucleic acid sequence, encoding a matureFactor IX polypeptide, that has at least 95%, 96%, 97%, 98%, 99%, 99.5%,99.9%, or 100% identity to CS03-MP-NA (SEQ ID NO: 14). In someembodiments, the FIX coding sequence portion of the polynucleotide alsoincludes a nucleic acid sequence, encoding a Factor IX signal peptide,that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to oneof FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25), CS03-SP-NA (SEQID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ ID NO:28), andCS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIX coding sequenceportion of the polynucleotide also includes a nucleic acid sequence,encoding a Factor IX pro-peptide (optionally in combination with anucleic acid sequence for a Factor IX signal peptide, as describedabove), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identityto one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ ID NO:31),CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA (SEQ IDNO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, the FIXcoding sequence portion of the polynucleotide includes a nucleic acidsequence, encoding a pre-pro-Factor IX polypeptide, that has at least95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity to CS03-FL-NA(SEQ ID NO:6).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a polynucleotide of structure C(e.g., a single-stranded polynucleotide), where the FIX coding sequenceportion of the polynucleotide includes a nucleic acid sequence, encodinga mature Factor IX polypeptide, that has at least 95%, 96%, 97%, 98%,99%, 99.5%, 99.9%, or 100% identity to CS03-MP-NA (SEQ ID NO:14). Insome embodiments, the FIX coding sequence portion of the polynucleotidealso includes a nucleic acid sequence, encoding a Factor IX signalpeptide, that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identity to one of FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25),CS03-SP-NA (SEQ ID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ IDNO:28), and CS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIXcoding sequence portion of the polynucleotide also includes a nucleicacid sequence, encoding a Factor IX pro-peptide (optionally incombination with a nucleic acid sequence for a Factor IX signal peptide,as described above), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identity to one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ IDNO:31), CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA(SEQ ID NO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, theFIX coding sequence portion of the polynucleotide includes a nucleicacid sequence, encoding a pre-pro-Factor IX polypeptide, that has atleast 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity toCS03-FL-NA (SEQ ID NO:6).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a polynucleotide of structure D(e.g., a single-stranded polynucleotide), where the FIX coding sequenceportion of the polynucleotide includes a nucleic acid sequence, encodinga mature Factor IX polypeptide, that has at least 95%, 96%, 97%, 98%,99%, 99.5%, 99.9%, or 100% identity to CS03-MP-NA (SEQ ID NO:14). Insome embodiments, the FIX coding sequence portion of the polynucleotidealso includes a nucleic acid sequence, encoding a Factor IX signalpeptide, that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identity to one of FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25),CS03-SP-NA (SEQ ID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ IDNO:28), and CS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIXcoding sequence portion of the polynucleotide also includes a nucleicacid sequence, encoding a Factor IX pro-peptide (optionally incombination with a nucleic acid sequence for a Factor IX signal peptide,as described above), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identity to one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ IDNO:31), CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA(SEQ ID NO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, theFIX coding sequence portion of the polynucleotide includes a nucleicacid sequence, encoding a pre-pro-Factor IX polypeptide, that has atleast 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity toCS03-FL-NA (SEQ ID NO:6).

CS04 Codon Altered Polynucleotides

In one embodiment, a nucleic acid composition provided herein includes aFactor IX polynucleotide (e.g., a codon-altered polynucleotide) encodinga single-chain Factor IX polypeptide, where the Factor IX polynucleotideincludes a nucleotide sequence having high sequence identity toCS04-FL-NA (SEQ ID NO:7). In some embodiments, the nucleotide sequenceof the Factor IX polynucleotide having high sequence identity toCS04-FL-NA (SEQ ID NO:7) has a reduced GC content, as compared to thewild-type Factor IX coding sequence (FIX-FL-NA (SEQ ID NO:1)). In someembodiments, the nucleotide sequence of the Factor IX polynucleotidehaving high sequence identity to CS04-FL-NA (SEQ ID NO:7) has a reducednumber of CpG dinucleotides, as compared to the wild-type Factor IXcoding sequence (FIX-FL-NA (SEQ ID NO: 1)).

In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 95% identity to CS04-FL-NA (SEQ ID NO:7). Ina specific embodiment, the sequence of the codon-altered polynucleotidehas at least 96% identity to CS04-FL-NA (SEQ ID NO:7). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 97% identity to CS04-FL-NA (SEQ ID NO:7). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 98% identity to CS04-FL-NA (SEQ ID NO:7). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 99% identity to CS04-FL-NA (SEQ ID NO:7). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 99.5% identity to CS04-FL-NA (SEQ ID NO:7). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 99.9% identity to CS04-FL-NA (SEQ ID NO:7). In another specificembodiment, the sequence of the codon-altered polynucleotide isCS04-FL-NA (SEQ ID NO:7).

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-FL-NA (SEQ ID NO:7) has a GCcontent of less than 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-FL-NA(SEQ ID NO:7) has a GC content of less than 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS04-FL-NA (SEQ ID NO:7) has a GC content of less than 58%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-FL-NA (SEQ ID NO:7) has a GCcontent of less than 57%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-FL-NA(SEQ ID NO:7) has a GC content of less than 56%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS04-FL-NA (SEQ ID NO:7) has a GC content of less than 55%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-FL-NA (SEQ ID NO:7) has a GCcontent of less than 54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-FL-NA (SEQ ID NO:7) has a GCcontent of from 50% to 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-FL-NA(SEQ ID NO:7) has a GC content of from 50% to 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS04-FL-NA (SEQ ID NO:7) has a GC content of from 50% to58%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS04-FL-NA (SEQ ID NO:7)has a GC content of from 50% to 57%. In some embodiments, the sequenceof the codon-altered polynucleotide having high sequence identity toCS04-FL-NA (SEQ ID NO:7) has a GC content of from 50% to 56%. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS04-FL-NA (SEQ ID NO:7) has a GC content offrom 50% to 55%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS04-FL-NA (SEQ ID NO:7)has a GC content of from 50% to 54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-FL-NA (SEQ ID NO:7) has a GCcontent of 53.8%±1.0. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-FL-NA(SEQ ID NO:7) has a GC content of 53.8%±0.8. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS04-FL-NA (SEQ ID NO:7) has a GC content of 53.8%±0.6. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-FL-NA (SEQ ID NO:7) has a GCcontent of 53.8%±0.5. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-FL-NA(SEQ ID NO:7) has a GC content of 53.8%±0.4. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS04-FL-NA (SEQ ID NO:7) has a GC content of 53.8%±0.3. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-FL-NA (SEQ ID NO:7) has a GCcontent of 53.8%±0.2. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-FL-NA(SEQ ID NO:7) has a GC content of 53.8%±0.1. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS04-FL-NA (SEQ ID NO:7) has a GC content of 53.8%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-FL-NA (SEQ ID NO:7) has no morethan 15 CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-FL-NA(SEQ ID NO:7) has no more than 12 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS04-FL-NA (SEQ ID NO:7) has no more than 10CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-FL-NA(SEQ ID NO:7) has no more than 9 CpG dinucleotides. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS04-FL-NA (SEQ ID NO:7) has no more than 8 CpGdinucleotides. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS04-FL-NA (SEQ ID NO:7)has no more than 7 CpG dinucleotides. In some embodiments, the sequenceof the codon-altered polynucleotide having high sequence identity toCS04-FL-NA (SEQ ID NO:7) has no more than 6 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS04-FL-NA (SEQ ID NO:7) has no more than 5CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-FL-NA(SEQ ID NO:7) has no more than 4 CpG dinucleotides. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS04-FL-NA (SEQ ID NO:7) has no more than 3 CpGdinucleotides. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS04-FL-NA (SEQ ID NO:7)has no more than 2 CpG dinucleotides. In some embodiments, the sequenceof the codon-altered polynucleotide having high sequence identity toCS04-FL-NA (SEQ ID NO:7) has no more than 1 CpG dinucleotide. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS04-FL-NA (SEQ ID NO:7) has no CpGdinucleotides.

In some embodiments, the encoded Factor IX polypeptide, e.g., thepolypeptide encoded by the polynucleotide having high sequence homologyto CS04-FL-NA (SEQ ID NO:7), has high sequence identity to the wild typeFactor IX pre-pro-protein sequence FIX-FL-AA (SEQ ID NO:2) and/or thePadua (hFIX(R384L)) pre-pro-protein sequence FIXp-FL-AA (SEQ ID NO:4).The encoded Factor IX polypeptide should retain the ability to becomeactivated into a function Factor IXa protein (e.g., by removal of thesignal peptide and the pro-peptide, and by excision of the activationpolypeptide).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIX-FL-AA (SEQ ID NO:2). In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 90% identityto FIX-FL-AA (SEQ ID NO:2). In one embodiment, the sequence of theencoded Factor IX polypeptide has at least 95% identity to FIX-FL-AA(SEQ ID NO:2). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 96% identity to FIX-FL-AA (SEQ ID NO:2). In oneembodiment, the sequence of the encoded Factor IX polypeptide has atleast 97% identity to FIX-FL-AA (SEQ ID NO:2). In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 98% identityto FIX-FL-AA (SEQ ID NO:2). In one embodiment, the sequence of theencoded Factor IX polypeptide has at least 99% identity to FIX-FL-AA(SEQ ID NO:2). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 99.5% identity to FIX-FL-AA (SEQ ID NO:2). Inone embodiment, the sequence of the encoded Factor IX polypeptide has atleast 99.9% identity to FIX-FL-AA (SEQ ID NO:2). In one embodiment, thesequence of the encoded Factor IX polypeptide is FIX-FL-AA (SEQ IDNO:2).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIXp-FL-AA (SEQ ID NO:4) and includes a leucineat position 384 of the pre-pro-polypeptide (e.g., position 338 of themature Factor IX single-chain polypeptide FIXp-MP-AA (SEQ ID NO: 12)).In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 90% identity to FIXp-FL-AA (SEQ ID NO:4) and includes a leucineat position 384 of the pre-pro-polypeptide. In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 95% identityto FIXp-FL-AA (SEQ ID NO:4) and includes a leucine at position 384 ofthe pre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 96% identity to FIXp-FL-AA (SEQ IDNO:4) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 97% identity FIXp-FL-AA (SEQ ID NO:4) and includes a leucine atposition 384 of the pre-pro-polypeptide. In one embodiment, the sequenceof the encoded Factor IX polypeptide has at least 98% identity toFIXp-FL-AA (SEQ ID NO:4) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 99% identity to FIXp-FL-AA (SEQ IDNO:4) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 99.5% identity to FIXp-FL-AA (SEQ ID NO:4) and includes aleucine at position 384 of the pre-pro-polypeptide. In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 99.9%identity to FIXp-FL-AA (SEQ ID NO:4) and includes a leucine at position384 of the pre-pro-polypeptide. In one embodiment, the sequence of theencoded Factor IX polypeptide is FIXp-FL-AA (SEQ ID NO:4).

In one embodiment, a nucleic acid composition provided herein includes aFactor IX polynucleotide (e.g., a codon-altered polynucleotide) encodinga single-chain Factor IX polypeptide (e.g., having serine proteaseactivity), where the Factor IX polynucleotide includes a nucleotidesequence having high sequence identity to CS04-MP-NA (SEQ ID NO:15). Insome embodiments, the nucleotide sequence of the Factor IXpolynucleotide having high sequence identity to CS04-MP-NA (SEQ IDNO:15) has a reduced GC content, as compared to the wild-type Factor IXcoding sequence (FIX-FL-NA (SEQ ID NO:1)). In some embodiments, thenucleotide sequence of the Factor IX polynucleotide having high sequenceidentity to CS04-MP-NA (SEQ ID NO:15) has a reduced number of CpGdinucleotides, as compared to the wild-type Factor IX coding sequence(FIX-FL-NA (SEQ ID NO: 1)).

In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 95% identity to CS04-MP-NA (SEQ ID NO:15).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 96% identity to CS04-MP-NA (SEQ ID NO:15).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 97% identity to CS04-MP-NA (SEQ ID NO: 15).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 98% identity to CS04-MP-NA (SEQ ID NO:15).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 99% identity to CS04-MP-NA (SEQ ID NO:15).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 99.5% identity to CS04-MP-NA (SEQ ID NO:15).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 99.9% identity to CS04-MP-NA (SEQ ID NO:15).In another specific embodiment, the sequence of the codon-alteredpolynucleotide is CS04-MP-NA (SEQ ID NO:15).

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-MP-NA (SEQ ID NO:15) has a GCcontent of less than 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-MP-NA(SEQ ID NO:15) has a GC content of less than 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS04-MP-NA (SEQ ID NO:15) has a GC content of less than 58%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-MP-NA (SEQ ID NO:15) has a GCcontent of less than 57%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-MP-NA(SEQ ID NO: 15) has a GC content of less than 56%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS04-MP-NA (SEQ ID NO:15) has a GC content of less than 55%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-MP-NA (SEQ ID NO:15) has a GCcontent of less than 54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-MP-NA (SEQ ID NO:15) has a GCcontent of from 50% to 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-MP-NA(SEQ ID NO:15) has a GC content of from 50% to 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS04-MP-NA (SEQ ID NO:15) has a GC content of from 50% to58%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS04-MP-NA (SEQ IDNO:15) has a GC content of from 50% to 57%. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS04-MP-NA (SEQ ID NO: 15) has a GC content of from 50% to56%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS04-MP-NA (SEQ ID NO:15) has a GC content of from 50% to 55%. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS04-MP-NA (SEQ ID NO: 15) has a GC content of from 50% to54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-MP-NA (SEQ ID NO:15) has a GCcontent of 53.8%±1.0. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-MP-NA(SEQ ID NO:15) has a GC content of 53.8%±0.8. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS04-MP-NA (SEQ ID NO:15) has a GC content of 53.8%±0.6. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-MP-NA (SEQ ID NO:15) has a GCcontent of 53.8%±0.5. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-MP-NA(SEQ ID NO: 15) has a GC content of 53.8%±0.4. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS04-MP-NA (SEQ ID NO:15) has a GC content of 53.8%±0.3. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-MP-NA (SEQ ID NO: 15) has a GCcontent of 53.8%±0.2. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-MP-NA(SEQ ID NO:15) has a GC content of 53.8%±0.1. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS04-MP-NA (SEQ ID NO:15) has a GC content of 53.8%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS04-MP-NA (SEQ ID NO:15) has no morethan 15 CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-MP-NA(SEQ ID NO:15) has no more than 12 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS04-MP-NA (SEQ ID NO:15) has no more than 10CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-MP-NA(SEQ ID NO:15) has no more than 9 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS04-MP-NA (SEQ ID NO: 15) has no more than 8CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-MP-NA(SEQ ID NO: 15) has no more than 7 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS04-MP-NA (SEQ ID NO:15) has no more than 6CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-MP-NA(SEQ ID NO:15) has no more than 5 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS04-MP-NA (SEQ ID NO:15) has no more than 4CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-MP-NA(SEQ ID NO:15) has no more than 3 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS04-MP-NA (SEQ ID NO:15) has no more than 2CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS04-MP-NA(SEQ ID NO: 15) has no more than 1 CpG dinucleotide. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS04-MP-NA (SEQ ID NO:15) has no CpGdinucleotides.

In some embodiments, the Factor IX polynucleotide high sequence identityto CS04-MP-NA (SEQ ID NO:15) further includes a Factor IX signalpolynucleotide encoding a Factor IX signal peptide having the amino acidsequence of FIX-SP-AA (SEQ ID NO:37). In some embodiments, the Factor IXsignal polynucleotide has a nucleic acid sequence that is at least 90%,95%, 96%, 97%, 98%, 99%, or 100% identical to CS02-SP-NA (SEQ ID NO:25).In some embodiments, the Factor IX signal polynucleotide has a nucleicacid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identical to CS03-SP-NA (SEQ ID NO:26). In some embodiments, the FactorIX signal polynucleotide has a nucleic acid sequence that is at least90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS04-SP-NA (SEQ IDNO:27). In some embodiments, the Factor IX signal polynucleotide has anucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identical to CS05-SP-NA (SEQ ID NO:28). In some embodiments, theFactor IX signal polynucleotide has a nucleic acid sequence that is atleast 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS06-SP-NA (SEQID NO:29).

In some embodiments, the Factor IX polynucleotide high sequence identityto CS04-MP-NA (SEQ ID NO:15) further includes a Factor IX pro-peptidepolynucleotide encoding a Factor IX pro-peptide having the amino acidsequence of FIX-PP-AA (SEQ ID NO:38). In some embodiments, the Factor IXpro-peptide polynucleotide has a nucleic acid sequence that is at least90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS02-PP-NA (SEQ IDNO:31). In some embodiments, the Factor IX pro-peptide polynucleotidehas a nucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%,99%, or 100% identical to CS03-PP-NA (SEQ ID NO:32). In someembodiments, the Factor IX pro-peptide polynucleotide has a nucleic acidsequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identical to CS04-PP-NA (SEQ ID NO:33). In some embodiments, the FactorIX pro-peptide polynucleotide has a nucleic acid sequence that is atleast 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS05-PP-NA (SEQID NO:34). In some embodiments, the Factor IX pro-peptide polynucleotidehas a nucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%,99%, or 100% identical to CS06-PP-NA (SEQ ID NO:35).

In some embodiments, the Factor IX polynucleotide high sequence identityto CS04-MP-NA (SEQ ID NO: 15) further includes a Factor IXpre-pro-peptide polynucleotide encoding a Factor IX pre-pro-peptidehaving the amino acid sequence of FIX-PPP-AA (SEQ ID NO:36). In someembodiments, the Factor IX pre-pro-peptide polynucleotide has a nucleicacid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identical to CS02-PPP-NA (SEQ ID NO:19). In some embodiments, the FactorIX pre-pro-peptide polynucleotide has a nucleic acid sequence that is atleast 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS03-PPP-NA(SEQ ID NO:20). In some embodiments, the Factor IX pre-pro-peptidepolynucleotide has a nucleic acid sequence that is at least 90%, 95%,96%, 97%, 98%, 99%, or 100% identical to CS04-PPP-NA (SEQ ID NO:21). Insome embodiments, the Factor IX pre-pro-peptide polynucleotide has anucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identical to CS05-PPP-NA (SEQ ID NO:22). In some embodiments, theFactor IX pre-pro-peptide polynucleotide has a nucleic acid sequencethat is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical toCS06-PPP-NA (SEQ ID NO:23).

In some embodiments, the encoded Factor IX polypeptide, e.g., thepolypeptide encoded by the polynucleotide having high sequence homologyto CS04-FL-NA (SEQ ID NO:7), has high sequence identity to the wildtype, mature Factor IX single-chain polypeptide sequence FIX-MP-AA (SEQID NO: 10) and/or the mature Padua (hFIX(R384L)) single-chain sequenceFIXp-MP-AA (SEQ ID NO: 12). The encoded Factor IX polypeptide shouldretain the ability to become activated into a function Factor IXaprotein (e.g., by removal of any signal peptide and the pro-peptide, andby excision of the activation polypeptide).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 90%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 95% identity to FIX-MP-AA(SEQ ID NO: 10). In one embodiment, the sequence of the encoded FactorIX polypeptide has at least 96% identity to FIX-MP-AA (SEQ ID NO: 10).In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 97% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 98%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 99% identity to FIX-MP-AA(SEQ ID NO:10). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 99.5% identity to FIX-MP-AA (SEQ ID NO: 10). Inone embodiment, the sequence of the encoded Factor IX polypeptide has atleast 99.9% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide is FIX-MP-AA (SEQ IDNO: 10).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide (e.g., position 338of the mature Factor IX single-chain polypeptide FIXp-MP-AA (SEQ ID NO:12)). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 90% identity to FIXp-MP-AA (SEQ ID NO: 12) andincludes a leucine at position 384 of the pre-pro-polypeptide. In oneembodiment, the sequence of the encoded Factor IX polypeptide has atleast 95% identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucineat position 384 of the pre-pro-polypeptide. In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 96% identityto FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 ofthe pre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 97% identity FIXp-MP-AA (SEQ ID NO:12) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 98% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide. In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 99%identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine atposition 384 of the pre-pro-polypeptide. In one embodiment, the sequenceof the encoded Factor IX polypeptide has at least 99.5% identity toFIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 99.9% identity to FIXp-MP-AA (SEQ IDNO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide is FIXp-MP-AA (SEQ ID NO: 12).

In one embodiment, a codon-altered polynucleotides provided hereinencodes for a single-chain Factor IX polypeptide including a lightchain, a heavy chain, and a polypeptide linker joining the C-terminus ofthe light chain to the N-terminus of the heavy chain. The light chain ofthe Factor IX polypeptide is encoded by a first nucleotide sequencehaving high sequence identity to CS04-LC-NA (SEQ ID NO:46), which is theportion of CS04-FL-NA (SEQ ID NO:7) encoding the Factor IX light chain.The heavy chain of the Factor IX polypeptide is encoded by a secondnucleotide sequence having high sequence identity to CS04-HC-NA (SEQ IDNO:45), which is the portion of CS04-FL-NA (SEQ ID NO:7) encoding theFactor IX heavy chain. The polypeptide linker includes Factor XIcleavage sites, which allow for maturation in vivo (e.g., afterexpression of the precursor single-chain Factor IX polypeptide.

In some embodiments, the first and second nucleotide sequences have atleast 95% sequence identity to CS04-LC-NA and CS04-HC-NA (SEQ ID NOS:46and 45), respectively. In some embodiments, the first and secondnucleotide sequences have at least 96% sequence identity to CS04-LC-NAand CS04-HC-NA (SEQ ID NOS:46 and 45), respectively. In someembodiments, the first and second nucleotide sequences have at least 97%sequence identity to CS04-LC-NA and CS04-HC-NA (SEQ ID NOS:46 and 45),respectively. In some embodiments, the first and second nucleotidesequences have at least 98% sequence identity to CS04-LC-NA andCS04-HC-NA (SEQ ID NOS:46 and 45), respectively. In some embodiments,the first and second nucleotide sequences have at least 99% sequenceidentity to CS04-LC-NA and CS04-HC-NA (SEQ ID NOS:46 and 45),respectively, respectively. In some embodiments, the first and secondnucleotide sequences have at least 99.5% sequence identity to CS04-LC-NAand CS04-HC-NA (SEQ ID NOS:46 and 45), respectively. In someembodiments, the first and second nucleotide sequences have at least99.9% sequence identity to CS04-LC-NA and CS04-HC-NA (SEQ ID NOS:46 and45), respectively. In some embodiments, the first and second nucleotidesequences are CS04-LC-NA and CS04-HC-NA (SEQ ID NOS:46 and 45),respectively.

In some embodiments, the polypeptide linker of the Factor IX constructis encoded by a third nucleotide sequence having high sequence identityto CS04-AP-NA (SEQ ID NO:59), which is a codon-altered sequence encodingthe wild type Factor IX activation polypeptide, e.g., amino acids192-226 of FIX-FL-AA (SEQ ID NO:2). In some embodiments, the thirdnucleotide sequence has at least 80% identity to CS04-AP-NA (SEQ IDNO:59). In some embodiments, the third nucleotide sequence has at least90% identity to CS04-AP-NA (SEQ ID NO:59). In some embodiments, thethird nucleotide sequence has at least 95% identity to CS04-AP-NA (SEQID NO:59). In some embodiments, the third nucleotide sequence has atleast 96% identity to CS04-AP-NA (SEQ ID NO:59). In some embodiments,the third nucleotide sequence has at least 97% identity to CS04-AP-NA(SEQ ID NO:59). In some embodiments, the third nucleotide sequence hasat least 98% identity to CS04-AP-NA (SEQ ID NO:59). In some embodiments,the third nucleotide sequence has at least 99% identity to CS04-AP-NA(SEQ ID NO:59). In some embodiments, the third nucleotide sequence isCS04-AP-NA (SEQ ID NO:59).

In some embodiments, the encoded Factor IX polypeptide also includes asignal peptide (e.g., a Factor IX signal peptide) and/or a pro-peptide(e.g., a Factor IX pro-peptide). In some embodiments, the signal peptideis the wild-type Factor IX signal peptide (FIX-SP-AA (SEQ ID NO:37)). Insome embodiments, the signal peptide is encoded by a codon-alteredpolynucleotide sequence having high sequence identity (e.g., at least95%, 96%, 97%, 98%, or 99%) to CS04-SP-NA (SEQ ID NO:27). In someembodiments, the pro-peptide is the wild-type Factor IX pro-peptide(FIX-PP-AA (SEQ ID NO:38)). In some embodiments, the pro-peptide peptideis encoded by a codon-altered polynucleotide sequence having highsequence identity (e.g., at least 95%, 96%, 97%, 98%, or 99%) toCS04-PP-NA (SEQ ID NO:33).

In some embodiments, the encoded Factor IX polypeptide, e.g., thepolypeptide encoded by the polynucleotide having high sequence homologyto CS04-LC-NA (SEQ ID NO:46) and CS04-HC-NA (SEQ ID NO:45), has highsequence identity to the wild type, mature Factor IX single-chainpolypeptide sequence FIX-MP-AA (SEQ ID NO:10) and/or the mature Padua(hFIX(R384L)) single-chain sequence FIXp-MP-AA (SEQ ID NO: 12). Theencoded Factor IX polypeptide should retain the ability to becomeactivated into a function Factor IXa protein (e.g., by removal of anysignal peptide and the pro-peptide, and by excision of the activationpolypeptide).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 90%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 95% identity to FIX-MP-AA(SEQ ID NO: 10). In one embodiment, the sequence of the encoded FactorIX polypeptide has at least 96% identity to FIX-MP-AA (SEQ ID NO: 10).In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 97% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 98%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 99% identity to FIX-MP-AA(SEQ ID NO:10). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 99.5% identity to FIX-MP-AA (SEQ ID NO: 10). Inone embodiment, the sequence of the encoded Factor IX polypeptide has atleast 99.9% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide is FIX-MP-AA (SEQ IDNO: 10).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide (e.g., position 338of the mature Factor IX single-chain polypeptide FIXp-MP-AA (SEQ ID NO:12)). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 90% identity to FIXp-MP-AA (SEQ ID NO: 12) andincludes a leucine at position 384 of the pre-pro-polypeptide. In oneembodiment, the sequence of the encoded Factor IX polypeptide has atleast 95% identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucineat position 384 of the pre-pro-polypeptide. In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 96% identityto FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 ofthe pre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 97% identity FIXp-MP-AA (SEQ ID NO:12) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 98% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide. In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 99%identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine atposition 384 of the pre-pro-polypeptide. In one embodiment, the sequenceof the encoded Factor IX polypeptide has at least 99.5% identity toFIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 99.9% identity to FIXp-MP-AA (SEQ IDNO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide is FIXp-MP-AA (SEQ ID NO: 12).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a self-complementarypolynucleotide of structure A, where the FIX coding sequence portion ofthe polynucleotide includes a nucleic acid sequence, encoding a matureFactor IX polypeptide, that has at least 95%, 96%, 97%, 98%, 99%, 99.5%,99.9%, or 100% identity to CS04-MP-NA (SEQ ID NO: 15). In someembodiments, the FIX coding sequence portion of the polynucleotide alsoincludes a nucleic acid sequence, encoding a Factor IX signal peptide,that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to oneof FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25), CS03-SP-NA (SEQID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ ID NO:28), andCS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIX coding sequenceportion of the polynucleotide also includes a nucleic acid sequence,encoding a Factor IX pro-peptide (optionally in combination with anucleic acid sequence for a Factor IX signal peptide, as describedabove), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identityto one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ ID NO:31),CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA (SEQ IDNO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, the FIXcoding sequence portion of the polynucleotide includes a nucleic acidsequence, encoding a pre-pro-Factor IX polypeptide, that has at least95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity to CS04-FL-NA(SEQ ID NO:7).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a self-complementarypolynucleotide of structure B, where the FIX coding sequence portion ofthe polynucleotide includes a nucleic acid sequence, encoding a matureFactor IX polypeptide, that has at least 95%, 96%, 97%, 98%, 99%, 99.5%,99.9%, or 100% identity to CS04-MP-NA (SEQ ID NO: 15). In someembodiments, the FIX coding sequence portion of the polynucleotide alsoincludes a nucleic acid sequence, encoding a Factor IX signal peptide,that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to oneof FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25), CS03-SP-NA (SEQID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ ID NO:28), andCS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIX coding sequenceportion of the polynucleotide also includes a nucleic acid sequence,encoding a Factor IX pro-peptide (optionally in combination with anucleic acid sequence for a Factor IX signal peptide, as describedabove), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identityto one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ ID NO:31),CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA (SEQ IDNO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, the FIXcoding sequence portion of the polynucleotide includes a nucleic acidsequence, encoding a pre-pro-Factor IX polypeptide, that has at least95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity to CS04-FL-NA(SEQ ID NO:7).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a polynucleotide of structure C(e.g., a single-stranded polynucleotide), where the FIX coding sequenceportion of the polynucleotide includes a nucleic acid sequence, encodinga mature Factor IX polypeptide, that has at least 95%, 96%, 97%, 98%,99%, 99.5%, 99.9%, or 100% identity to CS04-MP-NA (SEQ ID NO:15). Insome embodiments, the FIX coding sequence portion of the polynucleotidealso includes a nucleic acid sequence, encoding a Factor IX signalpeptide, that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identity to one of FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25),CS03-SP-NA (SEQ ID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ IDNO:28), and CS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIXcoding sequence portion of the polynucleotide also includes a nucleicacid sequence, encoding a Factor IX pro-peptide (optionally incombination with a nucleic acid sequence for a Factor IX signal peptide,as described above), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identity to one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ IDNO:31), CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA(SEQ ID NO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, theFIX coding sequence portion of the polynucleotide includes a nucleicacid sequence, encoding a pre-pro-Factor IX polypeptide, that has atleast 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity toCS04-FL-NA (SEQ ID NO:7).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a polynucleotide of structure D(e.g., a single-stranded polynucleotide), where the FIX coding sequenceportion of the polynucleotide includes a nucleic acid sequence, encodinga mature Factor IX polypeptide, that has at least 95%, 96%, 97%, 98%,99%, 99.5%, 99.9%, or 100% identity to CS04-MP-NA (SEQ ID NO:15). Insome embodiments, the FIX coding sequence portion of the polynucleotidealso includes a nucleic acid sequence, encoding a Factor IX signalpeptide, that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identity to one of FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25),CS03-SP-NA (SEQ ID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ IDNO:28), and CS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIXcoding sequence portion of the polynucleotide also includes a nucleicacid sequence, encoding a Factor IX pro-peptide (optionally incombination with a nucleic acid sequence for a Factor IX signal peptide,as described above), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identity to one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ IDNO:31), CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA(SEQ ID NO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, theFIX coding sequence portion of the polynucleotide includes a nucleicacid sequence, encoding a pre-pro-Factor IX polypeptide, that has atleast 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity toCS04-FL-NA (SEQ ID NO:7).

CS05 Codon Altered Polynucleotides

In one embodiment, a nucleic acid composition provided herein includes aFactor IX polynucleotide (e.g., a codon-altered polynucleotide) encodinga single-chain Factor IX polypeptide, where the Factor IX polynucleotideincludes a nucleotide sequence having high sequence identity toCS05-FL-NA (SEQ ID NO:8). In some embodiments, the nucleotide sequenceof the Factor IX polynucleotide having high sequence identity toCS05-FL-NA (SEQ ID NO:8) has a reduced GC content, as compared to thewild-type Factor IX coding sequence (FIX-FL-NA (SEQ ID NO:1)). In someembodiments, the nucleotide sequence of the Factor IX polynucleotidehaving high sequence identity to CS05-FL-NA (SEQ ID NO:8) has a reducednumber of CpG dinucleotides, as compared to the wild-type Factor IXcoding sequence (FIX-FL-NA (SEQ ID NO: 1)).

In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 95% identity to CS05-FL-NA (SEQ ID NO:8). Ina specific embodiment, the sequence of the codon-altered polynucleotidehas at least 96% identity to CS05-FL-NA (SEQ ID NO:8). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 97% identity to CS05-FL-NA (SEQ ID NO:8). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 98% identity to CS05-FL-NA (SEQ ID NO:8). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 99% identity to CS05-FL-NA (SEQ ID NO:8). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 99.5% identity to CS05-FL-NA (SEQ ID NO:8). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 99.9% identity to CS05-FL-NA (SEQ ID NO:8). In another specificembodiment, the sequence of the codon-altered polynucleotide isCS05-FL-NA (SEQ ID NO:8).

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-FL-NA (SEQ ID NO:8) has a GCcontent of less than 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-FL-NA(SEQ ID NO:8) has a GC content of less than 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS05-FL-NA (SEQ ID NO:8) has a GC content of less than 58%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-FL-NA (SEQ ID NO:8) has a GCcontent of less than 57%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-FL-NA(SEQ ID NO:8) has a GC content of less than 56%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS05-FL-NA (SEQ ID NO:8) has a GC content of less than 55%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-FL-NA (SEQ ID NO:8) has a GCcontent of less than 54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-FL-NA (SEQ ID NO:8) has a GCcontent of from 50% to 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-FL-NA(SEQ ID NO:8) has a GC content of from 50% to 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS05-FL-NA (SEQ ID NO:8) has a GC content of from 50% to58%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS05-FL-NA (SEQ ID NO:8)has a GC content of from 50% to 57%. In some embodiments, the sequenceof the codon-altered polynucleotide having high sequence identity toCS05-FL-NA (SEQ ID NO:8) has a GC content of from 50% to 56%. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS05-FL-NA (SEQ ID NO:8) has a GC content offrom 50% to 55%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS05-FL-NA (SEQ ID NO:8)has a GC content of from 50% to 54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-FL-NA (SEQ ID NO:8) has a GCcontent of 53.8%±1.0. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-FL-NA(SEQ ID NO:8) has a GC content of 53.8%±0.8. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS05-FL-NA (SEQ ID NO:8) has a GC content of 53.8%±0.6. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-FL-NA (SEQ ID NO:8) has a GCcontent of 53.8%±0.5. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-FL-NA(SEQ ID NO:8) has a GC content of 53.8%±0.4. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS05-FL-NA (SEQ ID NO:8) has a GC content of 53.8%±0.3. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-FL-NA (SEQ ID NO:8) has a GCcontent of 53.8%±0.2. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-FL-NA(SEQ ID NO:8) has a GC content of 53.8%±0.1. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS05-FL-NA (SEQ ID NO:8) has a GC content of 53.8%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-FL-NA (SEQ ID NO:8) has no morethan 15 CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-FL-NA(SEQ ID NO:8) has no more than 12 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS05-FL-NA (SEQ ID NO:8) has no more than 10CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-FL-NA(SEQ ID NO:8) has no more than 9 CpG dinucleotides. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS05-FL-NA (SEQ ID NO:8) has no more than 8 CpGdinucleotides. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS05-FL-NA (SEQ ID NO:8)has no more than 7 CpG dinucleotides. In some embodiments, the sequenceof the codon-altered polynucleotide having high sequence identity toCS05-FL-NA (SEQ ID NO:8) has no more than 6 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS05-FL-NA (SEQ ID NO:8) has no more than 5CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-FL-NA(SEQ ID NO:8) has no more than 4 CpG dinucleotides. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS05-FL-NA (SEQ ID NO:8) has no more than 3 CpGdinucleotides. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS05-FL-NA (SEQ ID NO:8)has no more than 2 CpG dinucleotides. In some embodiments, the sequenceof the codon-altered polynucleotide having high sequence identity toCS05-FL-NA (SEQ ID NO:8) has no more than 1 CpG dinucleotide. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS05-FL-NA (SEQ ID NO:8) has no CpGdinucleotides.

In some embodiments, the encoded Factor IX polypeptide, e.g., thepolypeptide encoded by the polynucleotide having high sequence homologyto CS05-FL-NA (SEQ ID NO:8), has high sequence identity to the wild typeFactor IX pre-pro-protein sequence FIX-FL-AA (SEQ ID NO:2) and/or thePadua (hFIX(R384L)) pre-pro-protein sequence FIXp-FL-AA (SEQ ID NO:4).The encoded Factor IX polypeptide should retain the ability to becomeactivated into a function Factor IXa protein (e.g., by removal of thesignal peptide and the pro-peptide, and by excision of the activationpolypeptide).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIX-FL-AA (SEQ ID NO:2). In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 90% identityto FIX-FL-AA (SEQ ID NO:2). In one embodiment, the sequence of theencoded Factor IX polypeptide has at least 95% identity to FIX-FL-AA(SEQ ID NO:2). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 96% identity to FIX-FL-AA (SEQ ID NO:2). In oneembodiment, the sequence of the encoded Factor IX polypeptide has atleast 97% identity to FIX-FL-AA (SEQ ID NO:2). In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 98% identityto FIX-FL-AA (SEQ ID NO:2). In one embodiment, the sequence of theencoded Factor IX polypeptide has at least 99% identity to FIX-FL-AA(SEQ ID NO:2). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 99.5% identity to FIX-FL-AA (SEQ ID NO:2). Inone embodiment, the sequence of the encoded Factor IX polypeptide has atleast 99.9% identity to FIX-FL-AA (SEQ ID NO:2). In one embodiment, thesequence of the encoded Factor IX polypeptide is FIX-FL-AA (SEQ IDNO:2).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIXp-FL-AA (SEQ ID NO:4) and includes a leucineat position 384 of the pre-pro-polypeptide (e.g., position 338 of themature Factor IX single-chain polypeptide FIXp-MP-AA (SEQ ID NO: 12)).In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 90% identity to FIXp-FL-AA (SEQ ID NO:4) and includes a leucineat position 384 of the pre-pro-polypeptide. In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 95% identityto FIXp-FL-AA (SEQ ID NO:4) and includes a leucine at position 384 ofthe pre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 96% identity to FIXp-FL-AA (SEQ IDNO:4) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 97% identity FIXp-FL-AA (SEQ ID NO:4) and includes a leucine atposition 384 of the pre-pro-polypeptide. In one embodiment, the sequenceof the encoded Factor IX polypeptide has at least 98% identity toFIXp-FL-AA (SEQ ID NO:4) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 99% identity to FIXp-FL-AA (SEQ IDNO:4) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 99.5% identity to FIXp-FL-AA (SEQ ID NO:4) and includes aleucine at position 384 of the pre-pro-polypeptide. In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 99.9%identity to FIXp-FL-AA (SEQ ID NO:4) and includes a leucine at position384 of the pre-pro-polypeptide. In one embodiment, the sequence of theencoded Factor IX polypeptide is FIXp-FL-AA (SEQ ID NO:4).

In one embodiment, a nucleic acid composition provided herein includes aFactor IX polynucleotide (e.g., a codon-altered polynucleotide) encodinga single-chain Factor IX polypeptide (e.g., having serine proteaseactivity), where the Factor IX polynucleotide includes a nucleotidesequence having high sequence identity to CS05-MP-NA (SEQ ID NO: 16). Insome embodiments, the nucleotide sequence of the Factor IXpolynucleotide having high sequence identity to CS05-MP-NA (SEQ IDNO:16) has a reduced GC content, as compared to the wild-type Factor IXcoding sequence (FIX-FL-NA (SEQ ID NO:1)). In some embodiments, thenucleotide sequence of the Factor IX polynucleotide having high sequenceidentity to CS05-MP-NA (SEQ ID NO: 16) has a reduced number of CpGdinucleotides, as compared to the wild-type Factor IX coding sequence(FIX-FL-NA (SEQ ID NO: 1)).

In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 95% identity to CS05-MP-NA (SEQ ID NO:16).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 96% identity to CS05-MP-NA (SEQ ID NO:16).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 97% identity to CS05-MP-NA (SEQ ID NO: 16).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 98% identity to CS05-MP-NA (SEQ ID NO:16).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 99% identity to CS05-MP-NA (SEQ ID NO:16).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 99.5% identity to CS05-MP-NA (SEQ ID NO:16).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 99.9% identity to CS05-MP-NA (SEQ ID NO:16).In another specific embodiment, the sequence of the codon-alteredpolynucleotide is CS05-MP-NA (SEQ ID NO:16).

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-MP-NA (SEQ ID NO:16) has a GCcontent of less than 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-MP-NA(SEQ ID NO:16) has a GC content of less than 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS05-MP-NA (SEQ ID NO:16) has a GC content of less than 58%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-MP-NA (SEQ ID NO: 16) has a GCcontent of less than 57%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-MP-NA(SEQ ID NO: 16) has a GC content of less than 56%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS05-MP-NA (SEQ ID NO:16) has a GC content of less than 55%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-MP-NA (SEQ ID NO:16) has a GCcontent of less than 54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-MP-NA (SEQ ID NO: 16) has a GCcontent of from 50% to 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-MP-NA(SEQ ID NO:16) has a GC content of from 50% to 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS05-MP-NA (SEQ ID NO: 16) has a GC content of from 50% to58%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS05-MP-NA (SEQ ID NO:16) has a GC content of from 50% to 57%. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS05-MP-NA (SEQ ID NO: 16) has a GC content of from 50% to56%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS05-MP-NA (SEQ ID NO:16) has a GC content of from 50% to 55%. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS05-MP-NA (SEQ ID NO: 16) has a GC content of from 50% to54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-MP-NA (SEQ ID NO:16) has a GCcontent of 53.8%±1.0. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-MP-NA(SEQ ID NO:16) has a GC content of 53.8%±0.8. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS05-MP-NA (SEQ ID NO:16) has a GC content of 53.8%±0.6. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-MP-NA (SEQ ID NO: 16) has a GCcontent of 53.8%±0.5. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-MP-NA(SEQ ID NO: 16) has a GC content of 53.8%±0.4. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS05-MP-NA (SEQ ID NO:16) has a GC content of 53.8%±0.3. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-MP-NA (SEQ ID NO: 16) has a GCcontent of 53.8%±0.2. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-MP-NA(SEQ ID NO:16) has a GC content of 53.8%±0.1. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS05-MP-NA (SEQ ID NO: 16) has a GC content of 53.8%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS05-MP-NA (SEQ ID NO:16) has no morethan 15 CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-MP-NA(SEQ ID NO:16) has no more than 12 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS05-MP-NA (SEQ ID NO:16) has no more than 10CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-MP-NA(SEQ ID NO:16) has no more than 9 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS05-MP-NA (SEQ ID NO: 16) has no more than 8CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-MP-NA(SEQ ID NO: 16) has no more than 7 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS05-MP-NA (SEQ ID NO:16) has no more than 6CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-MP-NA(SEQ ID NO: 16) has no more than 5 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS05-MP-NA (SEQ ID NO:16) has no more than 4CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-MP-NA(SEQ ID NO:16) has no more than 3 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS05-MP-NA (SEQ ID NO:16) has no more than 2CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS05-MP-NA(SEQ ID NO: 16) has no more than 1 CpG dinucleotide. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS05-MP-NA (SEQ ID NO:16) has no CpGdinucleotides.

In some embodiments, the Factor IX polynucleotide high sequence identityto CS05-MP-NA (SEQ ID NO:16) further includes a Factor IX signalpolynucleotide encoding a Factor IX signal peptide having the amino acidsequence of FIX-SP-AA (SEQ ID NO:37). In some embodiments, the Factor IXsignal polynucleotide has a nucleic acid sequence that is at least 90%,95%, 96%, 97%, 98%, 99%, or 100% identical to CS02-SP-NA (SEQ ID NO:25).In some embodiments, the Factor IX signal polynucleotide has a nucleicacid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identical to CS03-SP-NA (SEQ ID NO:26). In some embodiments, the FactorIX signal polynucleotide has a nucleic acid sequence that is at least90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS04-SP-NA (SEQ IDNO:27). In some embodiments, the Factor IX signal polynucleotide has anucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identical to CS05-SP-NA (SEQ ID NO:28). In some embodiments, theFactor IX signal polynucleotide has a nucleic acid sequence that is atleast 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS06-SP-NA (SEQID NO:29).

In some embodiments, the Factor IX polynucleotide high sequence identityto CS05-MP-NA (SEQ ID NO:16) further includes a Factor IX pro-peptidepolynucleotide encoding a Factor IX pro-peptide having the amino acidsequence of FIX-PP-AA (SEQ ID NO:38). In some embodiments, the Factor IXpro-peptide polynucleotide has a nucleic acid sequence that is at least90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS02-PP-NA (SEQ IDNO:31). In some embodiments, the Factor IX pro-peptide polynucleotidehas a nucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%,99%, or 100% identical to CS03-PP-NA (SEQ ID NO:32). In someembodiments, the Factor IX pro-peptide polynucleotide has a nucleic acidsequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identical to CS04-PP-NA (SEQ ID NO:33). In some embodiments, the FactorIX pro-peptide polynucleotide has a nucleic acid sequence that is atleast 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS05-PP-NA (SEQID NO:34). In some embodiments, the Factor IX pro-peptide polynucleotidehas a nucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%,99%, or 100% identical to CS06-PP-NA (SEQ ID NO:35).

In some embodiments, the Factor IX polynucleotide high sequence identityto CS05-MP-NA (SEQ ID NO: 16) further includes a Factor IXpre-pro-peptide polynucleotide encoding a Factor IX pre-pro-peptidehaving the amino acid sequence of FIX-PPP-AA (SEQ ID NO:36). In someembodiments, the Factor IX pre-pro-peptide polynucleotide has a nucleicacid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identical to CS02-PPP-NA (SEQ ID NO:19). In some embodiments, the FactorIX pre-pro-peptide polynucleotide has a nucleic acid sequence that is atleast 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS03-PPP-NA(SEQ ID NO:20). In some embodiments, the Factor IX pre-pro-peptidepolynucleotide has a nucleic acid sequence that is at least 90%, 95%,96%, 97%, 98%, 99%, or 100% identical to CS04-PPP-NA (SEQ ID NO:21). Insome embodiments, the Factor IX pre-pro-peptide polynucleotide has anucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identical to CS05-PPP-NA (SEQ ID NO:22). In some embodiments, theFactor IX pre-pro-peptide polynucleotide has a nucleic acid sequencethat is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical toCS06-PPP-NA (SEQ ID NO:23).

In some embodiments, the encoded Factor IX polypeptide, e.g., thepolypeptide encoded by the polynucleotide having high sequence homologyto CS05-FL-NA (SEQ ID NO:8), has high sequence identity to the wildtype, mature Factor IX single-chain polypeptide sequence FIX-MP-AA (SEQID NO: 10) and/or the mature Padua (hFIX(R384L)) single-chain sequenceFIXp-MP-AA (SEQ ID NO: 12). The encoded Factor IX polypeptide shouldretain the ability to become activated into a function Factor IXaprotein (e.g., by removal of any signal peptide and the pro-peptide, andby excision of the activation polypeptide).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 90%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 95% identity to FIX-MP-AA(SEQ ID NO: 10). In one embodiment, the sequence of the encoded FactorIX polypeptide has at least 96% identity to FIX-MP-AA (SEQ ID NO: 10).In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 97% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 98%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 99% identity to FIX-MP-AA(SEQ ID NO:10). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 99.5% identity to FIX-MP-AA (SEQ ID NO: 10). Inone embodiment, the sequence of the encoded Factor IX polypeptide has atleast 99.9% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide is FIX-MP-AA (SEQ IDNO: 10).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide (e.g., position 338of the mature Factor IX single-chain polypeptide FIXp-MP-AA (SEQ ID NO:12)). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 90% identity to FIXp-MP-AA (SEQ ID NO: 12) andincludes a leucine at position 384 of the pre-pro-polypeptide. In oneembodiment, the sequence of the encoded Factor IX polypeptide has atleast 95% identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucineat position 384 of the pre-pro-polypeptide. In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 96% identityto FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 ofthe pre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 97% identity FIXp-MP-AA (SEQ ID NO:12) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 98% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide. In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 99%identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine atposition 384 of the pre-pro-polypeptide. In one embodiment, the sequenceof the encoded Factor IX polypeptide has at least 99.5% identity toFIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 99.9% identity to FIXp-MP-AA (SEQ IDNO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide is FIXp-MP-AA (SEQ ID NO: 12).

In one embodiment, a codon-altered polynucleotides provided hereinencodes for a single-chain Factor IX polypeptide including a lightchain, a heavy chain, and a polypeptide linker joining the C-terminus ofthe light chain to the N-terminus of the heavy chain. The light chain ofthe Factor IX polypeptide is encoded by a first nucleotide sequencehaving high sequence identity to CS05-LC-NA (SEQ ID NO:48), which is theportion of CS05-FL-NA (SEQ ID NO:8) encoding the Factor IX light chain.The heavy chain of the Factor IX polypeptide is encoded by a secondnucleotide sequence having high sequence identity to CS05-HC-NA (SEQ IDNO:47), which is the portion of CS05-FL-NA (SEQ ID NO:8) encoding theFactor IX heavy chain. The polypeptide linker includes Factor XIcleavage sites, which allow for maturation in vivo (e.g., afterexpression of the precursor single-chain Factor IX polypeptide.

In some embodiments, the first and second nucleotide sequences have atleast 95% sequence identity to CS05-LC-NA and CS05-HC-NA (SEQ ID NOS:48and 47), respectively. In some embodiments, the first and secondnucleotide sequences have at least 96% sequence identity to CS05-LC-NAand CS05-HC-NA (SEQ ID NOS:48 and 47), respectively. In someembodiments, the first and second nucleotide sequences have at least 97%sequence identity to CS05-LC-NA and CS05-HC-NA (SEQ ID NOS:48 and 47),respectively. In some embodiments, the first and second nucleotidesequences have at least 98% sequence identity to CS05-LC-NA andCS05-HC-NA (SEQ ID NOS:48 and 47), respectively. In some embodiments,the first and second nucleotide sequences have at least 99% sequenceidentity to CS05-LC-NA and CS05-HC-NA (SEQ ID NOS:48 and 47),respectively, respectively. In some embodiments, the first and secondnucleotide sequences have at least 99.5% sequence identity to CS05-LC-NAand CS05-HC-NA (SEQ ID NOS:48 and 47), respectively. In someembodiments, the first and second nucleotide sequences have at least99.9% sequence identity to CS05-LC-NA and CS05-HC-NA (SEQ ID NOS:48 and47), respectively. In some embodiments, the first and second nucleotidesequences are CS05-LC-NA and CS05-HC-NA (SEQ ID NOS:48 and 47),respectively.

In some embodiments, the polypeptide linker of the Factor IX constructis encoded by a third nucleotide sequence having high sequence identityto CS05-AP-NA (SEQ ID NO:60), which is a codon-altered sequence encodingthe wild type Factor IX activation polypeptide, e.g., amino acids192-226 of FIX-FL-AA (SEQ ID NO:2). In some embodiments, the thirdnucleotide sequence has at least 80% identity to CS05-AP-NA (SEQ IDNO:60). In some embodiments, the third nucleotide sequence has at least90% identity to CS05-AP-NA (SEQ ID NO:60). In some embodiments, thethird nucleotide sequence has at least 95% identity to CS05-AP-NA (SEQID NO:60). In some embodiments, the third nucleotide sequence has atleast 96% identity to CS05-AP-NA (SEQ ID NO:60). In some embodiments,the third nucleotide sequence has at least 97% identity to CS05-AP-NA(SEQ ID NO:60). In some embodiments, the third nucleotide sequence hasat least 98% identity to CS05-AP-NA (SEQ ID NO:60). In some embodiments,the third nucleotide sequence has at least 99% identity to CS05-AP-NA(SEQ ID NO:60). In some embodiments, the third nucleotide sequence isCS05-AP-NA (SEQ ID NO:60).

In some embodiments, the encoded Factor IX polypeptide also includes asignal peptide (e.g., a Factor IX signal peptide) and/or a pro-peptide(e.g., a Factor IX pro-peptide). In some embodiments, the signal peptideis the wild-type Factor IX signal peptide (FIX-SP-AA (SEQ ID NO:37)). Insome embodiments, the signal peptide is encoded by a codon-alteredpolynucleotide sequence having high sequence identity (e.g., at least95%, 96%, 97%, 98%, or 99%) to CS05-SP-NA (SEQ ID NO:28). In someembodiments, the pro-peptide is the wild-type Factor IX pro-peptide(FIX-PP-AA (SEQ ID NO:38)). In some embodiments, the pro-peptide peptideis encoded by a codon-altered polynucleotide sequence having highsequence identity (e.g., at least 95%, 96%, 97%, 98%, or 99%) toCS05-PP-NA (SEQ ID NO:34).

In some embodiments, the encoded Factor IX polypeptide, e.g., thepolypeptide encoded by the polynucleotide having high sequence homologyto CS05-LC-NA (SEQ ID NO:48) and CS05-HC-NA (SEQ ID NO:47), has highsequence identity to the wild type, mature Factor IX single-chainpolypeptide sequence FIX-MP-AA (SEQ ID NO:10) and/or the mature Padua(hFIX(R384L)) single-chain sequence FIXp-MP-AA (SEQ ID NO: 12). Theencoded Factor IX polypeptide should retain the ability to becomeactivated into a function Factor IXa protein (e.g., by removal of anysignal peptide and the pro-peptide, and by excision of the activationpolypeptide).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 90%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 95% identity to FIX-MP-AA(SEQ ID NO: 10). In one embodiment, the sequence of the encoded FactorIX polypeptide has at least 96% identity to FIX-MP-AA (SEQ ID NO: 10).In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 97% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 98%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 99% identity to FIX-MP-AA(SEQ ID NO:10). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 99.5% identity to FIX-MP-AA (SEQ ID NO: 10). Inone embodiment, the sequence of the encoded Factor IX polypeptide has atleast 99.9% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide is FIX-MP-AA (SEQ IDNO: 10).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide (e.g., position 338of the mature Factor IX single-chain polypeptide FIXp-MP-AA (SEQ ID NO:12)). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 90% identity to FIXp-MP-AA (SEQ ID NO: 12) andincludes a leucine at position 384 of the pre-pro-polypeptide. In oneembodiment, the sequence of the encoded Factor IX polypeptide has atleast 95% identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucineat position 384 of the pre-pro-polypeptide. In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 96% identityto FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 ofthe pre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 97% identity FIXp-MP-AA (SEQ ID NO:12) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 98% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide. In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 99%identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine atposition 384 of the pre-pro-polypeptide. In one embodiment, the sequenceof the encoded Factor IX polypeptide has at least 99.5% identity toFIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 99.9% identity to FIXp-MP-AA (SEQ IDNO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide is FIXp-MP-AA (SEQ ID NO: 12).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a self-complementarypolynucleotide of structure A, where the FIX coding sequence portion ofthe polynucleotide includes a nucleic acid sequence, encoding a matureFactor IX polypeptide, that has at least 95%, 96%, 97%, 98%, 99%, 99.5%,99.9%, or 100% identity to CS03-MP-NA (SEQ ID NO: 14). In someembodiments, the FIX coding sequence portion of the polynucleotide alsoincludes a nucleic acid sequence, encoding a Factor IX signal peptide,that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to oneof FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25), CS03-SP-NA (SEQID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ ID NO:28), andCS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIX coding sequenceportion of the polynucleotide also includes a nucleic acid sequence,encoding a Factor IX pro-peptide (optionally in combination with anucleic acid sequence for a Factor IX signal peptide, as describedabove), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identityto one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ ID NO:31),CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA (SEQ IDNO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, the FIXcoding sequence portion of the polynucleotide includes a nucleic acidsequence, encoding a pre-pro-Factor IX polypeptide, that has at least95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity to CS05-FL-NA(SEQ ID NO:8).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a self-complementarypolynucleotide of structure B, where the FIX coding sequence portion ofthe polynucleotide includes a nucleic acid sequence, encoding a matureFactor IX polypeptide, that has at least 95%, 96%, 97%, 98%, 99%, 99.5%,99.9%, or 100% identity to CS05-MP-NA (SEQ ID NO: 16). In someembodiments, the FIX coding sequence portion of the polynucleotide alsoincludes a nucleic acid sequence, encoding a Factor IX signal peptide,that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to oneof FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25), CS03-SP-NA (SEQID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ ID NO:28), andCS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIX coding sequenceportion of the polynucleotide also includes a nucleic acid sequence,encoding a Factor IX pro-peptide (optionally in combination with anucleic acid sequence for a Factor IX signal peptide, as describedabove), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identityto one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ ID NO:31),CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA (SEQ IDNO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, the FIXcoding sequence portion of the polynucleotide includes a nucleic acidsequence, encoding a pre-pro-Factor IX polypeptide, that has at least95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity to CS05-FL-NA(SEQ ID NO:8).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a polynucleotide of structure C(e.g., a single-stranded polynucleotide), where the FIX coding sequenceportion of the polynucleotide includes a nucleic acid sequence, encodinga mature Factor IX polypeptide, that has at least 95%, 96%, 97%, 98%,99%, 99.5%, 99.9%, or 100% identity to CS05-MP-NA (SEQ ID NO:16). Insome embodiments, the FIX coding sequence portion of the polynucleotidealso includes a nucleic acid sequence, encoding a Factor IX signalpeptide, that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identity to one of FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25),CS03-SP-NA (SEQ ID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ IDNO:28), and CS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIXcoding sequence portion of the polynucleotide also includes a nucleicacid sequence, encoding a Factor IX pro-peptide (optionally incombination with a nucleic acid sequence for a Factor IX signal peptide,as described above), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identity to one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ IDNO:31), CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA(SEQ ID NO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, theFIX coding sequence portion of the polynucleotide includes a nucleicacid sequence, encoding a pre-pro-Factor IX polypeptide, that has atleast 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity toCS05-FL-NA (SEQ ID NO:8).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a polynucleotide of structure D(e.g., a single-stranded polynucleotide), where the FIX coding sequenceportion of the polynucleotide includes a nucleic acid sequence, encodinga mature Factor IX polypeptide, that has at least 95%, 96%, 97%, 98%,99%, 99.5%, 99.9%, or 100% identity to CS05-MP-NA (SEQ ID NO:16). Insome embodiments, the FIX coding sequence portion of the polynucleotidealso includes a nucleic acid sequence, encoding a Factor IX signalpeptide, that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identity to one of FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25),CS03-SP-NA (SEQ ID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ IDNO:28), and CS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIXcoding sequence portion of the polynucleotide also includes a nucleicacid sequence, encoding a Factor IX pro-peptide (optionally incombination with a nucleic acid sequence for a Factor IX signal peptide,as described above), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identity to one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ IDNO:31), CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA(SEQ ID NO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, theFIX coding sequence portion of the polynucleotide includes a nucleicacid sequence, encoding a pre-pro-Factor IX polypeptide, that has atleast 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity toCS05-FL-NA (SEQ ID NO:8).

CS06 Codon Altered Polynucleotides

In one embodiment, a nucleic acid composition provided herein includes aFactor IX polynucleotide (e.g., a codon-altered polynucleotide) encodinga single-chain Factor IX polypeptide, where the Factor IX polynucleotideincludes a nucleotide sequence having high sequence identity toCS06-FL-NA (SEQ ID NO:9). In some embodiments, the nucleotide sequenceof the Factor IX polynucleotide having high sequence identity toCS06-FL-NA (SEQ ID NO:9) has a reduced GC content, as compared to thewild-type Factor IX coding sequence (FIX-FL-NA (SEQ ID NO:1)). In someembodiments, the nucleotide sequence of the Factor IX polynucleotidehaving high sequence identity to CS06-FL-NA (SEQ ID NO:9) has a reducednumber of CpG dinucleotides, as compared to the wild-type Factor IXcoding sequence (FIX-FL-NA (SEQ ID NO: 1)).

In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 95% identity to CS06-FL-NA (SEQ ID NO:9). Ina specific embodiment, the sequence of the codon-altered polynucleotidehas at least 96% identity to CS06-FL-NA (SEQ ID NO:9). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 97% identity to CS06-FL-NA (SEQ ID NO:9). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 98% identity to CS06-FL-NA (SEQ ID NO:9). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 99% identity to CS06-FL-NA (SEQ ID NO:9). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 99.5% identity to CS06-FL-NA (SEQ ID NO:9). In a specificembodiment, the sequence of the codon-altered polynucleotide has atleast 99.9% identity to CS06-FL-NA (SEQ ID NO:9). In another specificembodiment, the sequence of the codon-altered polynucleotide isCS06-FL-NA (SEQ ID NO:9).

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-FL-NA (SEQ ID NO:9) has a GCcontent of less than 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-FL-NA(SEQ ID NO:9) has a GC content of less than 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS06-FL-NA (SEQ ID NO:9) has a GC content of less than 58%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-FL-NA (SEQ ID NO:9) has a GCcontent of less than 57%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-FL-NA(SEQ ID NO:9) has a GC content of less than 56%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS06-FL-NA (SEQ ID NO:9) has a GC content of less than 55%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-FL-NA (SEQ ID NO:9) has a GCcontent of less than 54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-FL-NA (SEQ ID NO:9) has a GCcontent of from 50% to 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-FL-NA(SEQ ID NO:9) has a GC content of from 50% to 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS06-FL-NA (SEQ ID NO:9) has a GC content of from 50% to58%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS06-FL-NA (SEQ ID NO:9)has a GC content of from 50% to 57%. In some embodiments, the sequenceof the codon-altered polynucleotide having high sequence identity toCS06-FL-NA (SEQ ID NO:9) has a GC content of from 50% to 56%. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS06-FL-NA (SEQ ID NO:9) has a GC content offrom 50% to 55%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS06-FL-NA (SEQ ID NO:9)has a GC content of from 50% to 54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-FL-NA (SEQ ID NO:9) has a GCcontent of 53.8%±1.0. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-FL-NA(SEQ ID NO:9) has a GC content of 53.8%±0.8. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS06-FL-NA (SEQ ID NO:9) has a GC content of 53.8%±0.6. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-FL-NA (SEQ ID NO:9) has a GCcontent of 53.8%±0.5. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-FL-NA(SEQ ID NO:9) has a GC content of 53.8%±0.4. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS06-FL-NA (SEQ ID NO:9) has a GC content of 53.8%±0.3. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-FL-NA (SEQ ID NO:9) has a GCcontent of 53.8%±0.2. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-FL-NA(SEQ ID NO:9) has a GC content of 53.8%±0.1. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS06-FL-NA (SEQ ID NO:9) has a GC content of 53.8%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-FL-NA (SEQ ID NO:9) has no morethan 15 CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-FL-NA(SEQ ID NO:9) has no more than 12 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS06-FL-NA (SEQ ID NO:9) has no more than 10CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-FL-NA(SEQ ID NO:9) has no more than 9 CpG dinucleotides. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS06-FL-NA (SEQ ID NO:9) has no more than 8 CpGdinucleotides. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS06-FL-NA (SEQ ID NO:9)has no more than 7 CpG dinucleotides. In some embodiments, the sequenceof the codon-altered polynucleotide having high sequence identity toCS06-FL-NA (SEQ ID NO:9) has no more than 6 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS06-FL-NA (SEQ ID NO:9) has no more than 5CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-FL-NA(SEQ ID NO:9) has no more than 4 CpG dinucleotides. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS06-FL-NA (SEQ ID NO:9) has no more than 3 CpGdinucleotides. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS06-FL-NA (SEQ ID NO:9)has no more than 2 CpG dinucleotides. In some embodiments, the sequenceof the codon-altered polynucleotide having high sequence identity toCS06-FL-NA (SEQ ID NO:9) has no more than 1 CpG dinucleotide. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS06-FL-NA (SEQ ID NO:9) has no CpGdinucleotides.

In some embodiments, the encoded Factor IX polypeptide, e.g., thepolypeptide encoded by the polynucleotide having high sequence homologyto CS06-FL-NA (SEQ ID NO:9), has high sequence identity to the wild typeFactor IX pre-pro-protein sequence FIX-FL-AA (SEQ ID NO:2) and/or thePadua (hFIX(R384L)) pre-pro-protein sequence FIXp-FL-AA (SEQ ID NO:4).The encoded Factor IX polypeptide should retain the ability to becomeactivated into a function Factor IXa protein (e.g., by removal of thesignal peptide and the pro-peptide, and by excision of the activationpolypeptide).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIX-FL-AA (SEQ ID NO:2). In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 90% identityto FIX-FL-AA (SEQ ID NO:2). In one embodiment, the sequence of theencoded Factor IX polypeptide has at least 95% identity to FIX-FL-AA(SEQ ID NO:2). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 96% identity to FIX-FL-AA (SEQ ID NO:2). In oneembodiment, the sequence of the encoded Factor IX polypeptide has atleast 97% identity to FIX-FL-AA (SEQ ID NO:2). In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 98% identityto FIX-FL-AA (SEQ ID NO:2). In one embodiment, the sequence of theencoded Factor IX polypeptide has at least 99% identity to FIX-FL-AA(SEQ ID NO:2). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 99.5% identity to FIX-FL-AA (SEQ ID NO:2). Inone embodiment, the sequence of the encoded Factor IX polypeptide has atleast 99.9% identity to FIX-FL-AA (SEQ ID NO:2). In one embodiment, thesequence of the encoded Factor IX polypeptide is FIX-FL-AA (SEQ IDNO:2).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIXp-FL-AA (SEQ ID NO:4) and includes a leucineat position 384 of the pre-pro-polypeptide (e.g., position 338 of themature Factor IX single-chain polypeptide FIXp-MP-AA (SEQ ID NO: 12)).In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 90% identity to FIXp-FL-AA (SEQ ID NO:4) and includes a leucineat position 384 of the pre-pro-polypeptide. In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 95% identityto FIXp-FL-AA (SEQ ID NO:4) and includes a leucine at position 384 ofthe pre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 96% identity to FIXp-FL-AA (SEQ IDNO:4) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 97% identity FIXp-FL-AA (SEQ ID NO:4) and includes a leucine atposition 384 of the pre-pro-polypeptide. In one embodiment, the sequenceof the encoded Factor IX polypeptide has at least 98% identity toFIXp-FL-AA (SEQ ID NO:4) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 99% identity to FIXp-FL-AA (SEQ IDNO:4) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 99.5% identity to FIXp-FL-AA (SEQ ID NO:4) and includes aleucine at position 384 of the pre-pro-polypeptide. In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 99.9%identity to FIXp-FL-AA (SEQ ID NO:4) and includes a leucine at position384 of the pre-pro-polypeptide. In one embodiment, the sequence of theencoded Factor IX polypeptide is FIXp-FL-AA (SEQ ID NO:4).

In one embodiment, a nucleic acid composition provided herein includes aFactor IX polynucleotide (e.g., a codon-altered polynucleotide) encodinga single-chain Factor IX polypeptide (e.g., having serine proteaseactivity), where the Factor IX polynucleotide includes a nucleotidesequence having high sequence identity to CS06-MP-NA (SEQ ID NO: 17). Insome embodiments, the nucleotide sequence of the Factor IXpolynucleotide having high sequence identity to CS06-MP-NA (SEQ IDNO:17) has a reduced GC content, as compared to the wild-type Factor IXcoding sequence (FIX-FL-NA (SEQ ID NO:1)). In some embodiments, thenucleotide sequence of the Factor IX polynucleotide having high sequenceidentity to CS06-MP-NA (SEQ ID NO: 17) has a reduced number of CpGdinucleotides, as compared to the wild-type Factor IX coding sequence(FIX-FL-NA (SEQ ID NO: 1)).

In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 95% identity to CS06-MP-NA (SEQ ID NO:17).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 96% identity to CS06-MP-NA (SEQ ID NO:17).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 97% identity to CS06-MP-NA (SEQ ID NO: 17).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 98% identity to CS06-MP-NA (SEQ ID NO:17).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 99% identity to CS06-MP-NA (SEQ ID NO:17).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 99.5% identity to CS06-MP-NA (SEQ ID NO:17).In a specific embodiment, the sequence of the codon-alteredpolynucleotide has at least 99.9% identity to CS06-MP-NA (SEQ ID NO:17).In another specific embodiment, the sequence of the codon-alteredpolynucleotide is CS06-MP-NA (SEQ ID NO:17).

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-MP-NA (SEQ ID NO:17) has a GCcontent of less than 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-MP-NA(SEQ ID NO:17) has a GC content of less than 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS06-MP-NA (SEQ ID NO:17) has a GC content of less than 58%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-MP-NA (SEQ ID NO: 17) has a GCcontent of less than 57%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-MP-NA(SEQ ID NO: 17) has a GC content of less than 56%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS06-MP-NA (SEQ ID NO:17) has a GC content of less than 55%.In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-MP-NA (SEQ ID NO:17) has a GCcontent of less than 54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-MP-NA (SEQ ID NO: 17) has a GCcontent of from 50% to 60%. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-MP-NA(SEQ ID NO:17) has a GC content of from 50% to 59%. In some embodiments,the sequence of the codon-altered polynucleotide having high sequenceidentity to CS06-MP-NA (SEQ ID NO: 17) has a GC content of from 50% to58%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS06-MP-NA (SEQ ID NO:17) has a GC content of from 50% to 57%. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS06-MP-NA (SEQ ID NO: 17) has a GC content of from 50% to56%. In some embodiments, the sequence of the codon-alteredpolynucleotide having high sequence identity to CS06-MP-NA (SEQ ID NO:17) has a GC content of from 50% to 55%. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS06-MP-NA (SEQ ID NO: 17) has a GC content of from 50% to54%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-MP-NA (SEQ ID NO:17) has a GCcontent of 53.8%±1.0. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-MP-NA(SEQ ID NO:17) has a GC content of 53.8%±0.8. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS06-MP-NA (SEQ ID NO:17) has a GC content of 53.8%±0.6. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-MP-NA (SEQ ID NO: 17) has a GCcontent of 53.8%±0.5. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-MP-NA(SEQ ID NO: 17) has a GC content of 53.8%±0.4. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS06-MP-NA (SEQ ID NO:17) has a GC content of 53.8%±0.3. Insome embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-MP-NA (SEQ ID NO: 17) has a GCcontent of 53.8%±0.2. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-MP-NA(SEQ ID NO:17) has a GC content of 53.8%±0.1. In some embodiments, thesequence of the codon-altered polynucleotide having high sequenceidentity to CS06-MP-NA (SEQ ID NO: 17) has a GC content of 53.8%.

In some embodiments, the sequence of the codon-altered polynucleotidehaving high sequence identity to CS06-MP-NA (SEQ ID NO:17) has no morethan 15 CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-MP-NA(SEQ ID NO:17) has no more than 12 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS06-MP-NA (SEQ ID NO:17) has no more than 10CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-MP-NA(SEQ ID NO:17) has no more than 9 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS06-MP-NA (SEQ ID NO: 17) has no more than 8CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-MP-NA(SEQ ID NO: 17) has no more than 7 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS06-MP-NA (SEQ ID NO:17) has no more than 6CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-MP-NA(SEQ ID NO: 17) has no more than 5 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS06-MP-NA (SEQ ID NO:17) has no more than 4CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-MP-NA(SEQ ID NO:17) has no more than 3 CpG dinucleotides. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS06-MP-NA (SEQ ID NO:17) has no more than 2CpG dinucleotides. In some embodiments, the sequence of thecodon-altered polynucleotide having high sequence identity to CS06-MP-NA(SEQ ID NO: 17) has no more than 1 CpG dinucleotide. In someembodiments, the sequence of the codon-altered polynucleotide havinghigh sequence identity to CS06-MP-NA (SEQ ID NO:17) has no CpGdinucleotides.

In some embodiments, the Factor IX polynucleotide high sequence identityto CS06-MP-NA (SEQ ID NO:17) further includes a Factor IX signalpolynucleotide encoding a Factor IX signal peptide having the amino acidsequence of FIX-SP-AA (SEQ ID NO:37). In some embodiments, the Factor IXsignal polynucleotide has a nucleic acid sequence that is at least 90%,95%, 96%, 97%, 98%, 99%, or 100% identical to CS02-SP-NA (SEQ ID NO:25).In some embodiments, the Factor IX signal polynucleotide has a nucleicacid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identical to CS03-SP-NA (SEQ ID NO:26). In some embodiments, the FactorIX signal polynucleotide has a nucleic acid sequence that is at least90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS04-SP-NA (SEQ IDNO:27). In some embodiments, the Factor IX signal polynucleotide has anucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identical to CS05-SP-NA (SEQ ID NO:28). In some embodiments, theFactor IX signal polynucleotide has a nucleic acid sequence that is atleast 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS06-SP-NA (SEQID NO:29).

In some embodiments, the Factor IX polynucleotide high sequence identityto CS06-MP-NA (SEQ ID NO:17) further includes a Factor IX pro-peptidepolynucleotide encoding a Factor IX pro-peptide having the amino acidsequence of FIX-PP-AA (SEQ ID NO:38). In some embodiments, the Factor IXpro-peptide polynucleotide has a nucleic acid sequence that is at least90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS02-PP-NA (SEQ IDNO:31). In some embodiments, the Factor IX pro-peptide polynucleotidehas a nucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%,99%, or 100% identical to CS03-PP-NA (SEQ ID NO:32). In someembodiments, the Factor IX pro-peptide polynucleotide has a nucleic acidsequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identical to CS04-PP-NA (SEQ ID NO:33). In some embodiments, the FactorIX pro-peptide polynucleotide has a nucleic acid sequence that is atleast 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS05-PP-NA (SEQID NO:34). In some embodiments, the Factor IX pro-peptide polynucleotidehas a nucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%,99%, or 100% identical to CS06-PP-NA (SEQ ID NO:35).

In some embodiments, the Factor IX polynucleotide high sequence identityto CS06-MP-NA (SEQ ID NO: 17) further includes a Factor IXpre-pro-peptide polynucleotide encoding a Factor IX pre-pro-peptidehaving the amino acid sequence of FIX-PPP-AA (SEQ ID NO:36). In someembodiments, the Factor IX pre-pro-peptide polynucleotide has a nucleicacid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identical to CS02-PPP-NA (SEQ ID NO:19). In some embodiments, the FactorIX pre-pro-peptide polynucleotide has a nucleic acid sequence that is atleast 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to CS03-PPP-NA(SEQ ID NO:20). In some embodiments, the Factor IX pre-pro-peptidepolynucleotide has a nucleic acid sequence that is at least 90%, 95%,96%, 97%, 98%, 99%, or 100% identical to CS04-PPP-NA (SEQ ID NO:21). Insome embodiments, the Factor IX pre-pro-peptide polynucleotide has anucleic acid sequence that is at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identical to CS05-PPP-NA (SEQ ID NO:22). In some embodiments, theFactor IX pre-pro-peptide polynucleotide has a nucleic acid sequencethat is at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical toCS06-PPP-NA (SEQ ID NO:23).

In some embodiments, the encoded Factor IX polypeptide, e.g., thepolypeptide encoded by the polynucleotide having high sequence homologyto CS06-FL-NA (SEQ ID NO:9), has high sequence identity to the wildtype, mature Factor IX single-chain polypeptide sequence FIX-MP-AA (SEQID NO: 10) and/or the mature Padua (hFIX(R384L)) single-chain sequenceFIXp-MP-AA (SEQ ID NO: 12). The encoded Factor IX polypeptide shouldretain the ability to become activated into a function Factor IXaprotein (e.g., by removal of any signal peptide and the pro-peptide, andby excision of the activation polypeptide).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 90%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 95% identity to FIX-MP-AA(SEQ ID NO: 10). In one embodiment, the sequence of the encoded FactorIX polypeptide has at least 96% identity to FIX-MP-AA (SEQ ID NO: 10).In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 97% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 98%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 99% identity to FIX-MP-AA(SEQ ID NO:10). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 99.5% identity to FIX-MP-AA (SEQ ID NO: 10). Inone embodiment, the sequence of the encoded Factor IX polypeptide has atleast 99.9% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide is FIX-MP-AA (SEQ IDNO: 10).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide (e.g., position 338of the mature Factor IX single-chain polypeptide FIXp-MP-AA (SEQ ID NO:12)). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 90% identity to FIXp-MP-AA (SEQ ID NO: 12) andincludes a leucine at position 384 of the pre-pro-polypeptide. In oneembodiment, the sequence of the encoded Factor IX polypeptide has atleast 95% identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucineat position 384 of the pre-pro-polypeptide. In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 96% identityto FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 ofthe pre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 97% identity FIXp-MP-AA (SEQ ID NO:12) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 98% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide. In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 99%identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine atposition 384 of the pre-pro-polypeptide. In one embodiment, the sequenceof the encoded Factor IX polypeptide has at least 99.5% identity toFIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 99.9% identity to FIXp-MP-AA (SEQ IDNO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide is FIXp-MP-AA (SEQ ID NO: 12).

In one embodiment, a codon-altered polynucleotides provided hereinencodes for a single-chain Factor IX polypeptide including a lightchain, a heavy chain, and a polypeptide linker joining the C-terminus ofthe light chain to the N-terminus of the heavy chain. The light chain ofthe Factor IX polypeptide is encoded by a first nucleotide sequencehaving high sequence identity to CS06-LC-NA (SEQ ID NO:50), which is theportion of CS06-FL-NA (SEQ ID NO:9) encoding the Factor IX light chain.The heavy chain of the Factor IX polypeptide is encoded by a secondnucleotide sequence having high sequence identity to CS06-HC-NA (SEQ IDNO:49), which is the portion of CS06-FL-NA (SEQ ID NO:9) encoding theFactor IX heavy chain. The polypeptide linker includes Factor XIcleavage sites, which allow for maturation in vivo (e.g., afterexpression of the precursor single-chain Factor IX polypeptide.

In some embodiments, the first and second nucleotide sequences have atleast 95% sequence identity to CS06-LC-NA and CS06-HC-NA (SEQ ID NOS:50and 49), respectively. In some embodiments, the first and secondnucleotide sequences have at least 96% sequence identity to CS06-LC-NAand CS06-HC-NA (SEQ ID NOS:50 and 49), respectively. In someembodiments, the first and second nucleotide sequences have at least 97%sequence identity to CS06-LC-NA and CS06-HC-NA (SEQ ID NOS:50 and 49),respectively. In some embodiments, the first and second nucleotidesequences have at least 98% sequence identity to CS06-LC-NA andCS06-HC-NA (SEQ ID NOS:50 and 49), respectively. In some embodiments,the first and second nucleotide sequences have at least 99% sequenceidentity to CS06-LC-NA and CS06-HC-NA (SEQ ID NOS:50 and 49),respectively, respectively. In some embodiments, the first and secondnucleotide sequences have at least 99.5% sequence identity to CS06-LC-NAand CS06-HC-NA (SEQ ID NOS:50 and 49), respectively. In someembodiments, the first and second nucleotide sequences have at least99.9% sequence identity to CS06-LC-NA and CS06-HC-NA (SEQ ID NOS:50 and49), respectively. In some embodiments, the first and second nucleotidesequences are CS06-LC-NA and CS06-HC-NA (SEQ ID NOS:50 and 49),respectively.

In some embodiments, the polypeptide linker of the Factor IX constructis encoded by a third nucleotide sequence having high sequence identityto CS06-AP-NA (SEQ ID NO:61), which is a codon-altered sequence encodingthe wild type Factor IX activation polypeptide, e.g., amino acids192-226 of FIX-FL-AA (SEQ ID NO:2). In some embodiments, the thirdnucleotide sequence has at least 80% identity to CS06-AP-NA (SEQ IDNO:61). In some embodiments, the third nucleotide sequence has at least90% identity to CS06-AP-NA (SEQ ID NO:61). In some embodiments, thethird nucleotide sequence has at least 95% identity to CS06-AP-NA (SEQID NO:61). In some embodiments, the third nucleotide sequence has atleast 96% identity to CS06-AP-NA (SEQ ID NO:61). In some embodiments,the third nucleotide sequence has at least 97% identity to CS06-AP-NA(SEQ ID NO:61). In some embodiments, the third nucleotide sequence hasat least 98% identity to CS06-AP-NA (SEQ ID NO:61). In some embodiments,the third nucleotide sequence has at least 99% identity to CS06-AP-NA(SEQ ID NO:61). In some embodiments, the third nucleotide sequence isCS06-AP-NA (SEQ ID NO:61).

In some embodiments, the encoded Factor IX polypeptide also includes asignal peptide (e.g., a Factor IX signal peptide) and/or a pro-peptide(e.g., a Factor IX pro-peptide). In some embodiments, the signal peptideis the wild-type Factor IX signal peptide (FIX-SP-AA (SEQ ID NO:37)). Insome embodiments, the signal peptide is encoded by a codon-alteredpolynucleotide sequence having high sequence identity (e.g., at least95%, 96%, 97%, 98%, or 99%) to CS06-SP-NA (SEQ ID NO:29). In someembodiments, the pro-peptide is the wild-type Factor IX pro-peptide(FIX-PP-AA (SEQ ID NO:38)). In some embodiments, the pro-peptide peptideis encoded by a codon-altered polynucleotide sequence having highsequence identity (e.g., at least 95%, 96%, 97%, 98%, or 99%) toCS06-PP-NA (SEQ ID NO:35).

In some embodiments, the encoded Factor IX polypeptide, e.g., thepolypeptide encoded by the polynucleotide having high sequence homologyto CS06-LC-NA (SEQ ID NO:50) and CS06-HC-NA (SEQ ID NO:49), has highsequence identity to the wild type, mature Factor IX single-chainpolypeptide sequence FIX-MP-AA (SEQ ID NO:10) and/or the mature Padua(hFIX(R384L)) single-chain sequence FIXp-MP-AA (SEQ ID NO: 12). Theencoded Factor IX polypeptide should retain the ability to becomeactivated into a function Factor IXa protein (e.g., by removal of anysignal peptide and the pro-peptide, and by excision of the activationpolypeptide).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 90%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 95% identity to FIX-MP-AA(SEQ ID NO: 10). In one embodiment, the sequence of the encoded FactorIX polypeptide has at least 96% identity to FIX-MP-AA (SEQ ID NO: 10).In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 97% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 98%identity to FIX-MP-AA (SEQ ID NO:10). In one embodiment, the sequence ofthe encoded Factor IX polypeptide has at least 99% identity to FIX-MP-AA(SEQ ID NO:10). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 99.5% identity to FIX-MP-AA (SEQ ID NO: 10). Inone embodiment, the sequence of the encoded Factor IX polypeptide has atleast 99.9% identity to FIX-MP-AA (SEQ ID NO: 10). In one embodiment,the sequence of the encoded Factor IX polypeptide is FIX-MP-AA (SEQ IDNO: 10).

In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 85% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide (e.g., position 338of the mature Factor IX single-chain polypeptide FIXp-MP-AA (SEQ ID NO:12)). In one embodiment, the sequence of the encoded Factor IXpolypeptide has at least 90% identity to FIXp-MP-AA (SEQ ID NO: 12) andincludes a leucine at position 384 of the pre-pro-polypeptide. In oneembodiment, the sequence of the encoded Factor IX polypeptide has atleast 95% identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucineat position 384 of the pre-pro-polypeptide. In one embodiment, thesequence of the encoded Factor IX polypeptide has at least 96% identityto FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 ofthe pre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 97% identity FIXp-MP-AA (SEQ ID NO:12) and includes a leucine at position 384 of the pre-pro-polypeptide.In one embodiment, the sequence of the encoded Factor IX polypeptide hasat least 98% identity to FIXp-MP-AA (SEQ ID NO:12) and includes aleucine at position 384 of the pre-pro-polypeptide. In one embodiment,the sequence of the encoded Factor IX polypeptide has at least 99%identity to FIXp-MP-AA (SEQ ID NO: 12) and includes a leucine atposition 384 of the pre-pro-polypeptide. In one embodiment, the sequenceof the encoded Factor IX polypeptide has at least 99.5% identity toFIXp-MP-AA (SEQ ID NO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide has at least 99.9% identity to FIXp-MP-AA (SEQ IDNO: 12) and includes a leucine at position 384 of thepre-pro-polypeptide. In one embodiment, the sequence of the encodedFactor IX polypeptide is FIXp-MP-AA (SEQ ID NO: 12).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a self-complementarypolynucleotide of structure A, where the FIX coding sequence portion ofthe polynucleotide includes a nucleic acid sequence, encoding a matureFactor IX polypeptide, that has at least 95%, 96%, 97%, 98%, 99%, 99.5%,99.9%, or 100% identity to CS06-MP-NA (SEQ ID NO: 17). In someembodiments, the FIX coding sequence portion of the polynucleotide alsoincludes a nucleic acid sequence, encoding a Factor IX signal peptide,that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to oneof FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25), CS03-SP-NA (SEQID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ ID NO:28), andCS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIX coding sequenceportion of the polynucleotide also includes a nucleic acid sequence,encoding a Factor IX pro-peptide (optionally in combination with anucleic acid sequence for a Factor IX signal peptide, as describedabove), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identityto one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ ID NO:31),CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA (SEQ IDNO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, the FIXcoding sequence portion of the polynucleotide includes a nucleic acidsequence, encoding a pre-pro-Factor IX polypeptide, that has at least95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity to CS06-FL-NA(SEQ ID NO:9).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a self-complementarypolynucleotide of structure B, where the FIX coding sequence portion ofthe polynucleotide includes a nucleic acid sequence, encoding a matureFactor IX polypeptide, that has at least 95%, 96%, 97%, 98%, 99%, 99.5%,99.9%, or 100% identity to CS06-MP-NA (SEQ ID NO: 17). In someembodiments, the FIX coding sequence portion of the polynucleotide alsoincludes a nucleic acid sequence, encoding a Factor IX signal peptide,that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identity to oneof FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25), CS03-SP-NA (SEQID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ ID NO:28), andCS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIX coding sequenceportion of the polynucleotide also includes a nucleic acid sequence,encoding a Factor IX pro-peptide (optionally in combination with anucleic acid sequence for a Factor IX signal peptide, as describedabove), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% identityto one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ ID NO:31),CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA (SEQ IDNO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, the FIXcoding sequence portion of the polynucleotide includes a nucleic acidsequence, encoding a pre-pro-Factor IX polypeptide, that has at least95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity to CS06-FL-NA(SEQ ID NO:9).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a polynucleotide of structure C(e.g., a single-stranded polynucleotide), where the FIX coding sequenceportion of the polynucleotide includes a nucleic acid sequence, encodinga mature Factor IX polypeptide, that has at least 95%, 96%, 97%, 98%,99%, 99.5%, 99.9%, or 100% identity to CS06-MP-NA (SEQ ID NO:17). Insome embodiments, the FIX coding sequence portion of the polynucleotidealso includes a nucleic acid sequence, encoding a Factor IX signalpeptide, that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identity to one of FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25),CS03-SP-NA (SEQ ID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ IDNO:28), and CS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIXcoding sequence portion of the polynucleotide also includes a nucleicacid sequence, encoding a Factor IX pro-peptide (optionally incombination with a nucleic acid sequence for a Factor IX signal peptide,as described above), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identity to one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ IDNO:31), CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA(SEQ ID NO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, theFIX coding sequence portion of the polynucleotide includes a nucleicacid sequence, encoding a pre-pro-Factor IX polypeptide, that has atleast 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity toCS06-FL-NA (SEQ ID NO:9).

In some embodiments, with reference to FIG. 1, a nucleic acidcomposition is provided that includes a polynucleotide of structure D(e.g., a single-stranded polynucleotide), where the FIX coding sequenceportion of the polynucleotide includes a nucleic acid sequence, encodinga mature Factor IX polypeptide, that has at least 95%, 96%, 97%, 98%,99%, 99.5%, 99.9%, or 100% identity to CS06-MP-NA (SEQ ID NO:17). Insome embodiments, the FIX coding sequence portion of the polynucleotidealso includes a nucleic acid sequence, encoding a Factor IX signalpeptide, that has at least 90%, 95%, 96%, 97%, 98%, 99%, or 100%identity to one of FIX-SP-NA (SEQ ID NO:24), CS02-SP-NA (SEQ ID NO:25),CS03-SP-NA (SEQ ID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ IDNO:28), and CS06-SP-NA (SEQ ID NO:29). In some embodiments, the FIXcoding sequence portion of the polynucleotide also includes a nucleicacid sequence, encoding a Factor IX pro-peptide (optionally incombination with a nucleic acid sequence for a Factor IX signal peptide,as described above), that has at least 90%, 95%, 96%, 97%, 98%, 99%, or100% identity to one of FIX-PP-NA (SEQ ID NO:30), CS02-PP-NA (SEQ IDNO:31), CS03-PP-NA (SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA(SEQ ID NO:34), and CS06-PP-NA (SEQ ID NO:35). In some embodiments, theFIX coding sequence portion of the polynucleotide includes a nucleicacid sequence, encoding a pre-pro-Factor IX polypeptide, that has atleast 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100% identity toCS06-FL-NA (SEQ ID NO:9).

C. Codon-Altered Factor IX Signal and Pro-Peptides

In one aspect, the disclosure provides codon-altered polynucleotidesencoding Factor IX signal peptides, Factor IX pro-peptides, and both(e.g., Factor IX pre-pro-peptides). These codon-altered polynucleotidesimprove Factor IX expression and may be placed, e.g., upstream of apolynucleotide, codon-altered or otherwise, encoding a Factor IXsingle-chain polypeptide (e.g., a Factor IX light chain, activationpeptide, and heavy chain). Generally, the encoded peptides are wild-typeFactor IX signal peptides (e.g., FIX-SP-AA (SEQ ID NO:37)), pro-peptides(e.g., FIX-PP-AA (SEQ ID NO:38), and pre-pro-peptides (FIX-PPP-AA (SEQID NO:36)).

In certain embodiments, the codon-altered polynucleotides encodingFactor IX signal peptides, pro-peptides, and pre-pro-peptides have asequence with high identity (e.g., at least 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, or 100%) to one of CS02-SP-NA (SEQ ID NO:25),CS03-SP-NA (SEQ ID NO:26), CS04-SP-NA (SEQ ID NO:27), CS05-SP-NA (SEQ IDNO:28), CS06-SP-NA (SEQ ID NO:29), CS02-PP-NA (SEQ ID NO:31), CS03-PP-NA(SEQ ID NO:32), CS04-PP-NA (SEQ ID NO:33), CS05-PP-NA (SEQ ID NO:34),CS06-PP-NA (SEQ ID NO:35), CS02-PPP-NA (SEQ ID NO: 19), CS03-PPP-NA (SEQID NO:20), CS04-PPP-NA (SEQ ID NO:21), CS05-PPP-NA (SEQ ID NO:22), andCS06-PPP-NA (SEQ ID NO:23).

CS02 Signal and Pro-Peptides

In one embodiment, the codon-altered polynucleotide encoding a Factor IXsignal peptide has at least 95% sequence identity to CS02-SP-NA (SEQ IDNO:25). In other embodiments, the codon-altered polynucleotide encodinga Factor IX signal peptide has at least 96%, 97%, 98%, 99%, or 100%identity to CS02-SP-NA (SEQ ID NO:25).

In one embodiment, the codon-altered polynucleotide encoding a Factor IXpro-peptide has at least 95% sequence identity to CS02-PP-NA (SEQ IDNO:31). In other embodiments, the codon-altered polynucleotide encodinga Factor IX pro-peptide has at least 96%, 97%, 98%, 99%, or 100%identity to CS02-PP-NA (SEQ ID NO:31).

In one embodiment, the codon-altered polynucleotide encoding a Factor IXpre-pro-peptide has at least 95% sequence identity to CS02-PPP-NA (SEQID NO:19). In other embodiments, the codon-altered polynucleotideencoding a Factor IX pre-pro-peptide has at least 96%, 97%, 98%, 99%, or100% identity to CS02-PPP-NA (SEQ ID NO:19).

CS03 Signal and Pro-Peptides

In one embodiment, the codon-altered polynucleotide encoding a Factor IXsignal peptide has at least 95% sequence identity to CS03-SP-NA (SEQ IDNO:26). In other embodiments, the codon-altered polynucleotide encodinga Factor IX signal peptide has at least 96%, 97%, 98%, 99%, or 100%identity to CS03-SP-NA (SEQ ID NO:26).

In one embodiment, the codon-altered polynucleotide encoding a Factor IXpro-peptide has at least 95% sequence identity to CS03-PP-NA (SEQ IDNO:32). In other embodiments, the codon-altered polynucleotide encodinga Factor IX pro-peptide has at least 96%, 97%, 98%, 99%, or 100%identity to CS03-PP-NA (SEQ ID NO:32).

In one embodiment, the codon-altered polynucleotide encoding a Factor IXpre-pro-peptide has at least 95% sequence identity to CS03-PPP-NA (SEQID NO:20). In other embodiments, the codon-altered polynucleotideencoding a Factor IX pre-pro-peptide has at least 96%, 97%, 98%, 99%, or100% identity to CS03-PPP-NA (SEQ ID NO:20).

CS04 Signal and Pro-Peptides

In one embodiment, the codon-altered polynucleotide encoding a Factor IXsignal peptide has at least 95% sequence identity to CS04-SP-NA (SEQ IDNO:27). In other embodiments, the codon-altered polynucleotide encodinga Factor IX signal peptide has at least 96%, 97%, 98%, 99%, or 100%identity to CS04-SP-NA (SEQ ID NO:27).

In one embodiment, the codon-altered polynucleotide encoding a Factor IXpro-peptide has at least 95% sequence identity to CS04-PP-NA (SEQ IDNO:33). In other embodiments, the codon-altered polynucleotide encodinga Factor IX pro-peptide has at least 96%, 97%, 98%, 99%, or 100%identity to CS04-PP-NA (SEQ ID NO:33).

In one embodiment, the codon-altered polynucleotide encoding a Factor IXpre-pro-peptide has at least 95% sequence identity to CS04-PPP-NA (SEQID NO:21). In other embodiments, the codon-altered polynucleotideencoding a Factor IX pre-pro-peptide has at least 96%, 97%, 98%, 99%, or100% identity to CS04-PPP-NA (SEQ ID NO:21).

CS05 Signal and Pro-Peptides

In one embodiment, the codon-altered polynucleotide encoding a Factor IXsignal peptide has at least 95% sequence identity to CS05-SP-NA (SEQ IDNO:28). In other embodiments, the codon-altered polynucleotide encodinga Factor IX signal peptide has at least 96%, 97%, 98%, 99%, or 100%identity to CS05-SP-NA (SEQ ID NO:28).

In one embodiment, the codon-altered polynucleotide encoding a Factor IXpro-peptide has at least 95% sequence identity to CS05-PP-NA (SEQ IDNO:34). In other embodiments, the codon-altered polynucleotide encodinga Factor IX pro-peptide has at least 96%, 97%, 98%, 99%, or 100%identity to CS05-PP-NA (SEQ ID NO:34).

In one embodiment, the codon-altered polynucleotide encoding a Factor IXpre-pro-peptide has at least 95% sequence identity to CS05-PPP-NA (SEQID NO:22). In other embodiments, the codon-altered polynucleotideencoding a Factor IX pre-pro-peptide has at least 96%, 97%, 98%, 99%, or100% identity to CS05-PPP-NA (SEQ ID NO:22).

CS06 Signal and Pro-Peptides

In one embodiment, the codon-altered polynucleotide encoding a Factor IXsignal peptide has at least 95% sequence identity to CS06-SP-NA (SEQ IDNO:29). In other embodiments, the codon-altered polynucleotide encodinga Factor IX signal peptide has at least 96%, 97%, 98%, 99%, or 100%identity to CS06-SP-NA (SEQ ID NO:29).

In one embodiment, the codon-altered polynucleotide encoding a Factor IXpro-peptide has at least 95% sequence identity to CS06-PP-NA (SEQ IDNO:35). In other embodiments, the codon-altered polynucleotide encodinga Factor IX pro-peptide has at least 96%, 97%, 98%, 99%, or 100%identity to CS06-PP-NA (SEQ ID NO:35).

In one embodiment, the codon-altered polynucleotide encoding a Factor IXpre-pro-peptide has at least 95% sequence identity to CS06-PPP-NA (SEQID NO:23). In other embodiments, the codon-altered polynucleotideencoding a Factor IX pre-pro-peptide has at least 96%, 97%, 98%, 99%, or100% identity to CS06-PPP-NA (SEQ ID NO:23).

IV. Factor IX Expression Vectors

In some embodiments, the codon-altered polynucleotides described hereinare integrated into expression vectors. As will be appreciated by one ofskill in the art, many forms of vectors can be used to effectuate FactorIX gene therapy using the codon-altered Factor IX polynucleotidesequences disclosed herein. Non-limiting examples of expression vectorsinclude viral vectors (e.g., vectors suitable for gene therapy), plasmidvectors, bacteriophage vectors, cosmids, phagemids, artificialchromosomes, and the like.

In some embodiments, the codon-altered polynucleotides described hereinare integrated into a viral gene therapy vector. Non-limiting examplesof viral vectors include: retrovirus, e.g., Moloney murine leukemiavirus (MMLV), Harvey murine sarcoma virus, murine mammary tumor virus,and Rous sarcoma virus; adenoviruses, adeno-associated viruses;SV40-type viruses; polyomaviruses; Epstein-Barr viruses; papillomaviruses; herpes viruses; vaccinia viruses; and polio viruses.

In vivo, Factor IX is synthesized primarily in the liver. As such,hepatocytes have been targeted as suitable host cells for Factor IX genetherapy constructs. Several classes of viral vectors have been showncompetent for liver-targeted delivery of a gene therapy construct,including retroviral vectors (see, e.g., Axelrod et al., 1990; Kay etal., 1992; Van den Driessche et al., 1999, and Xu et al., 2003, 2005,the disclosures of which are hereby expressly incorporated by reference,in their entireties, for all purposes), lentiviral (see, e.g., Ward etal., 2011, Brown et al., 2007, and Matrai et al., 2011, the disclosuresof which are hereby expressly incorporated by reference, in theirentireties, for all purposes), adeno-associated viral (AAV) (see, e.g.,Herzog et al., 1999, the disclosure of which is hereby expresslyincorporated by reference, in its entirety, for all purposes), andadenoviral vectors (see, e.g., Brown et al., 2004 and Ehrhardt & Kay,2002, the disclosures of which are hereby expressly incorporated byreference, in their entireties, for all purposes).

In some embodiments, the gene therapy vector is a retrovirus, andparticularly a replication-deficient retrovirus. Protocols for theproduction of replication-deficient retroviruses are known in the art.For review, see Kriegler, M., Gene Transfer and Expression, A LaboratoryManual, W.H. Freeman Co., New York (1990) and Murry, E. J., Methods inMolecular Biology, Vol. 7, Humana Press, Inc., Cliffton, N.J. (1991).

In one embodiment, the gene therapy vector is an adeno-associated virus(AAV) based gene therapy vector. AAV systems have been describedpreviously and are generally well known in the art (Kelleher and Vos,Biotechniques, 17(6):1110-17 (1994); Cotten et al., P.N.A.S. U.S.A.,89(13):6094-98 (1992); Curiel, Nat Immun, 13(2-3):141-64 (1994);Muzyczka, Curr Top Microbiol Immunol, 158:97-129 (1992); and Asokan A,et al., Mol. Ther., 20(4):699-708 (2012), each incorporated herein byreference in their entireties for all purposes). Details concerning thegeneration and use of rAAV vectors are described, for example, in U.S.Pat. Nos. 5,139,941 and 4,797,368, each incorporated herein by referencein their entireties for all purposes. In a particular embodiment, theAAV vector is an AAV-8 vector.

An exemplary AAV delivery vector for liver-specific Factor IX expressionis described in WO 2009/130208, the content of which is expresslyincorporated by reference herein, in its entirety, for all purposes. Thevector is a single-stranded AAV vector encoding human Factor IX, andincludes TTR Serp regulatory sequences driving a factor cDNA. The vectoralso includes intron I of the human Factor IX gene and apoly-adenylation signal.

In some embodiments, the codon-altered polynucleotides described hereinare integrated into a retroviral expression vector. These systems havebeen described previously, and are generally well known in the art (Mannet al., Cell, 33:153-159, 1983; Nicolas and Rubinstein, In: Vectors: Asurvey of molecular cloning vectors and their uses, Rodriguez andDenhardt, eds., Stoneham: Butterworth, pp. 494-513, 1988; Temin, In:Gene Transfer, Kucherlapati (ed.), New York: Plenum Press, pp. 149-188,1986). In a specific embodiment, the retroviral vector is a lentiviralvector (see, for example, Naldini et al., Science, 272(5259):263-267,1996; Zufferey et al., Nat Biotechnol, 15(9):871-875, 1997; Blomer etal., J Virol., 71(9):6641-6649, 1997; U.S. Pat. Nos. 6,013,516 and5,994,136).

In some embodiments, the codon-altered polynucleotides described hereincan be administered to a subject by a non-viral method. For example,naked DNA can be administered into a cell by electroporation,sonoporation, particle bombarment, or hydrodyamic delivery. DNA can alsobe encapsulated or coupled with polymers, e.g., liposomes, polysomes,polypleses, dendrimers, and administered to the subject as a complex.Likewise, DNA can be coupled to inorganic nanoparticles, e.g., gold,silica, iron oxide, or calcium phosphate particles, or attached tocell-penetrating peptides for delivery to cells in vivo.

Codon-altered Factor IX coding polynucleotides can also be incorporatedinto artificial chromosomes, such as Artificial Chromosome Expression(ACEs) (see, e.g., Lindenbaum et al., Nucleic Acids Res., 32(21):e172(2004)) and mammalian artificial chromosomes (MACs). For review see,e.g., Perez-Luz and Diaz-Nido, J Biomed Biotechnol. 2010: Article ID642804 (2010).

A wide variety of vectors can be used for the expression of a Factor IXpolypeptide from a codon-altered polypeptide in cell culture, includingeukaryotic and prokaryotic expression vectors. In certain embodiments, aplasmid vector is contemplated for use in expressing a Factor IXpolypeptide in cell culture. In general, plasmid vectors containingreplicon and control sequences which are derived from species compatiblewith the host cell are used in connection with these hosts. The vectorcan carry a replication site, as well as marking sequences which arecapable of providing phenotypic selection in transformed cells. Theplasmid will include the codon-altered polynucleotide encoding theFactor IX polypeptide, operably linked to one or more control sequences,for example, a promoter.

Non-limiting examples of vectors for prokaryotic expression includeplasmids such as pRSET, pET, pBAD, etc., wherein the promoters used inprokaryotic expression vectors include lac, trc, trp, recA, araBAD, etc.Examples of vectors for eukaryotic expression include: (i) forexpression in yeast, vectors such as pAO, pPIC, pYES, pMET, usingpromoters such as AOX1, GAP, GAL 1, AUG1, etc; (ii) for expression ininsect cells, vectors such as pMT, pAc5, pIB, pMIB, pBAC, etc., usingpromoters such as PH, p10, MT, Ac5, OpIE2, gp64, polh, etc., and (iii)for expression in mammalian cells, vectors such as pSVL, pCMV, pRc/RSV,pcDNA3, pBPV, etc., and vectors derived from viral systems such asvaccinia virus, adeno-associated viruses, herpes viruses, retroviruses,etc., using promoters such as CMV, SV40, EF-1, UbC, RSV, ADV, BPV, andβ-actin.

In some embodiments, the disclosure provides an AAV gene therapy vectorthat includes a codon-altered Factor IX polynucleotide, as describedherein, internal terminal repeat (ITR) sequences on the 5′ and 3′ endsof the vector, one or more promoter and/or enhancer sequencesoperably-linked to the Factor IX polynucleotide, and a poly-adenylationsignal following the 3′ end of the Factor IX polynucleotide sequence. Insome embodiments, the one or more promoter and/or enhancer sequencesinclude one or more copies of a liver-specific regulatory controlelement.

FIG. 1 illustrates several exemplary architectures for a Factor IX genetherapy vector, in accordance with some implementations. FIG. 1Aillustrates a self-complementary AAV vector having a mutated 5′ ITR,truncated TTR enhancer/promoter sequences, an MVM viral intron sequence,a codon-altered Factor IX coding sequence, a poly-adenylation sequence,and a 3′-ITR. FIG. 1B illustrates a self-complementary AAV vectorencoding a Factor IX polypeptide similar to FIG. 1A, but furtherincluding one or more (e.g., one, two, three, or more) liver-specificregulatory control elements. FIG. 1C illustrates a single-strandedvector having the same elements as FIG. 1A, except that the 5′-ITR isnot mutated, preventing self-complementarity. FIG. 1D illustrates asingle-stranded AAV vector encoding a Factor IX polypeptide similar toFIG. 1A, but further including one or more (e.g., one, two, three, ormore) liver-specific regulatory control elements. Although illustratedwith reference to a Factor IX protein that includes an R384L ‘Padua’amino acid substitution in FIG. 1, in some embodiments, a Factor IXnucleotide construct having a general structure as depicted in FIG. 1(e.g., structure A, B, C, or D) encodes a Factor IX protein that doesnot include an R384L ‘Padua’ amino acid substitution.

FIG. 25 shows the nucleotide sequence of an AAV Factor IX gene therapyvector CS06-CRM8.3-ssV (SEQ ID NO:40), which exemplifies the genetherapy vector architecture illustrated in FIG. 1D. Nucleotides 1-145 ofCS06-CRM8.3-ssV (SEQ ID NO:40) is an AAV2 5′-ITR sequence (SEQ IDNO:51). The 5′-ITR sequence is followed by three copies of aliver-specific CRM8 regulatory control element CRM8 (SEQ ID NO:39) atnucleotides 165-236, 238-309, and 311-382. Following the CRM8 sequenceis a truncated TTR enhancer/promoter sequence (SEQ ID NO:52) atnucleotides 383-712. Next, the vector includes a minute virus of mice(MVM) intron (SEQ ID NO:53) at nucleotides 724-800. Nucleotides 814-2199of the vector are a CS06 codon-altered Factor IX(R384L) coding sequence(CS06-FL-NA (SEQ ID NO:9)). The Factor IX polynucleotide sequence isfollowed by a BGH poly-adenylation signal at nucleotides 2208-2441 and,finally, an AAV2 3′-ITR sequence (SEQ ID NO:55) at nucleotides2458-2602.

In some embodiments, the disclosure provides a Factor IX polynucleotidecomprising a sequence having at least 95% identity to nucleotides 1-2602of SEQ ID NO:40. In some embodiments, the disclosure provides a FactorIX polynucleotide comprising a sequence having at least 99% identity tonucleotides 1-2602 of SEQ ID NO:40. In some embodiments, the disclosureprovides a Factor IX polynucleotide comprising a sequence having atleast 99.5% identity to nucleotides 1-2602 of SEQ ID NO:40. In someembodiments, the disclosure provides a Factor IX polynucleotidecomprising the sequence of nucleotides 1-2602 of SEQ ID NO:40.

Several AAV serotypes have been characterized, including AAV1, AAV2,AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, and AAV9. Generally, any AAVserotype may be used for the Factor IX gene therapy constructs describedherein. However, the serotypes have different tropisms, e.g., theypreferentially infect different tissues. In one embodiment, becauseFactor IX is produced primarily in the liver, an AAV serotype for thedisclosed gene therapy constructs is selected based on a liver tropism,found in at least serotypes AAV7, AAV8, and AAV9. Accordingly, in oneembodiment, a Factor IX gene therapy construct is an AAV7 serotypevector. In another embodiment, a Factor IX gene therapy construct is anAAV8 serotype vector. In yet another embodiment, a Factor IX genetherapy construct is an AAV9 serotype vector.

The Factor IX gene therapy constructs described herein may besingle-stranded (e.g., a ssAAV vector, as illustrated in FIGS. 1C and1D) or self-complementary (e.g., a scAAV vector, as illustrated in FIGS.1A and 1B). Although research and theory has suggested thatself-complementary AAV vectors should facilitate better transgeneexpression, by bypassing the requirement for second-strand synthesisprior to translation, single-stranded AAV vectors promoting betterFactor IX expression that comparable self-complementary vector wereidentified, as reported in Example 5.

Promoters and Enhancers

The Factor IX gene therapy constructs described herein generally includeone or more promoter and/or enhancer element that drives gene expressionin vivo, e.g., a regulatory element. In some embodiments, a promoter orenhancer element drives expression in a tissue dependent fashion, e.g.,predominantly in a specific tissue. Because Factor IX is synthesizedprimarily in the liver, in some embodiments, the gene therapy vectorsdescribed herein include a liver-specific regulatory element, whichsubstantially limit expression of the gene therapy vector to hepaticcells.

Generally, liver-specific regulatory elements can be derived from anygene known to be exclusively expressed in the liver. WO 2009/130208identifies several genes expressed in a liver-specific fashion,including, serpin peptidase inhibitor, clade A member 1, also known asα-antitrypsin (SERPINA1; GeneID 5265), apolipoprotein C-I (APOC1; GeneID341), apolipoprotein C-IV (APOC4; GeneID 346), apolipoprotein H (APOH;GeneID 350); transthyretin (TTR; GeneID 7276), albumin (ALB; GeneID213), aldolase B (ALDOB; GeneID 229), cytochrome P450, family 2,subfamily E, polypeptide 1 (CYP2E1; GeneID 1571), fibrinogen alpha chain(FGA; GeneID 2243), transferrin (TF; GeneID 7018), haptoglobin relatedprotein (HPR; GeneID 3250). In some embodiments, the Factor IX genetherapy constructs described herein include a liver-specific regulatoryelement derived from the genomic loci of one or more of these proteins.Several examples of such elements are described in WO 2009/130208, thecontent of which is expressly incorporated herein by reference, in itsentirety, for all purposes.

One example of a liver-specific regulatory element is from thetransthyretin (TTR) gene, commonly referred to as “TTRe” or “TTREnh.”Hsieh J. L., et al., Cancer Sci., 100(3):537-45 (2009), the content ofwhich is expressly incorporated herein by reference, in its entirety,for all purposes. In some embodiments, the Factor IX gene therapyconstructs described herein include truncated TTR enhancer and promoterelements. An example of these elements is provided at nucleotides383-712 of CS06-CRM8.3-ssV (SEQ ID NO:40), provided as FIG. 25. In someembodiments, a truncated TTR enhancer and promoter element has at least85% sequence identity to nucleotides 383-712 of CS06-CRM8.3-ssV (SEQ IDNO:40). In other embodiments, the truncated TTR enhancer and promoterelement have at least 90%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 100%sequence identity to nucleotides 383-712 of CS06-CRM8.3-ssV (SEQ IDNO:40).

Another example of a liver-specific regulatory element is from theSERPINA1 gene, as described in PCT Publication No. WO 2016/146757, thecontent of which is expressly incorporated herein by reference, in itsentirety, for all purposes. An example of such an element is the CRM8regulatory control element (SEQ ID NO:39) provided at nucleotides165-236 of CS06-CRM8.3-ssV (SEQ ID NO:40). In some embodiments, aSERPINA1-derived regulatory control element has at least 85% sequenceidentity to CRM8 (SEQ ID NO:39). In other embodiments, the truncatedSERPINA1-derived regulatory control element has at least 90%, 95%, 96%,97%, 98%, 99%, or 100% sequence identity to CRM8 (SEQ ID NO:39).

In some embodiments, a Factor IX gene therapy construct includes one ormore SERPINA1-derived regulatory control element, as exemplified by theconstructs illustrated in FIGS. 1B and 1D. In one embodiment, aconstruct includes one SERPINA1-derived regulatory control element(e.g., CRM8). In another embodiment, a construct includes twoSERPINA1-derived regulatory control elements (e.g., CRM8). In anotherembodiment, a construct includes three SERPINA1-derived regulatorycontrol elements (e.g., CRM8). In yet other embodiments, a constructincludes 4, 5, 6, or more SERPINA1-derived regulatory control elements(e.g., CRM8).

In one embodiment, a Factor IX gene therapy construct includes one ormore SERPINA1-derived regulatory control element (e.g., CRM8) and atruncated TTR enhancer and promoter element, as exemplified in FIGS. 1B,1D, and 25.

Introns

In some embodiments, the Factor IX gene therapy constructs describedherein include an intron, e.g., a virally-derived intron, to increaseexpression of the Factor IX gene. Suitable introns for the expression ofgene therapy constructs are known in the art. Typically, the intron ispositioned 5′ of the transgene coding sequence, as exemplified in theFactor IX constructs shown in FIG. 1 and FIG. 25. However, in someembodiments, the intron may be positioned within the transgene codingsequence, e.g., at a natural Factor IX intron junction or otherwise, or3′ of the transgene coding sequence. Non-limiting examples of intronsthat can be used in the Factor IX gene therapy constructs describedherein include introns derived from a Minute Virus of Mice (MVM) intron,a beta-globin intron (betalVS-ll), a Factor IX (FIX) intron A, a Simianvirus 40 (SV40) Small T intron, and a beta-actin intron.

In one embodiment, the Factor IX gene therapy constructs describedherein include an MVM-derived intron, e.g., as illustrated in FIG. 1 andexemplified by the MVM intron (SEQ ID NO:53) at nucleotides 724-800 ofCS06-CRM8.3-ssV (SEQ ID NO:40) in FIG. 25. In some embodiments, anintron used in the gene therapy constructs described herein has at least85% sequence identity to MVM (SEQ ID NO:53). In other embodiments, anintron used in the gene therapy constructs described herein has at least90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to MVM (SEQ IDNO:53).

Poly-Adenylation Signals

In some embodiments, the Factor IX gene therapy constructs describedherein include a poly-adenylation signal, e.g., as illustrated in inFIG. 1. The poly-adenylation signal directs synthesis of a poly-A tailon the 3′ end of the mRNA transcript generated from the Factor IXtransgene. Accordingly, the poly-adenylation signal is positioned 3′ tothe Factor IX coding sequence. Non-limiting examples of poly-adenylationsignals that can be used in the Factor IX gene therapy constructsdescribed herein include poly-adenylation signals derived from a Simianvirus 40 (SV40) late gene, a bovine growth hormone (BGH) polyadenylationsignal, and a minimal rabbit β-globin (mRBG) gene.

In one embodiment, the Factor IX gene therapy constructs describedherein include a poly-adenylation signal derived from the bovine growthhormone (BGH) polyadenylation signal, e.g., as illustrated in FIG. 1 andexemplified by the BGHpA signal (SEQ ID NO:54) at nucleotides 2208-2441of CS06-CRM8.3-ssV (SEQ ID NO:40) in FIG. 25. In some embodiments, apoly-adenylation signal used in the gene therapy constructs describedherein has at least 85% sequence identity to the BGHpA signal (SEQ IDNO:54). In other embodiments, a poly-adenylation signal used in the genetherapy constructs described herein has at least 90%, 95%, 96%, 97%,98%, 99%, or 100% sequence identity to the BGHpA signal (SEQ ID NO:54).

V. Methods

Production

The codon-altered Factor IX polynucleotides and viral vectors describedherein (e.g., the nucleic acid compositions) are produced according toconventional methods for nucleic acid amplification and vectorproduction. Two predominant platforms have developed for large-scaleproduction of recombinant AAV vectors. The first platform is based onreplication in mammalian cells, while the second is based on replicationin invertebrate cells. For review, see, Kotin R. M., Hum. Mol. Genet.,20(R1):R2-6 (2011), the content of which is expressly incorporatedherein by reference, in its entirety, for all purposes.

Accordingly, the disclosure provides methods for producing anadeno-associated virus (AAV) particle. In some embodiments, the methodsinclude introducing a codon-altered Factor IX polynucleotide constructhaving high nucleotide sequence identity (e.g., at least 95%, 96%, 97%,98%, 99%, 99.5%, 99.9%, or 100%) to one of a CS02, CS03, CS04, CS05, orCS06 sequence, as described herein, into a host cell where thepolynucleotide construct is competent for replication in the host cell.

In some embodiments, the host cell is a mammalian host cell e.g., anHEK, CHO, or BHK cell. In a specific embodiment, the host cell is an HEK293 cell. In some embodiments, the host cell is an invertebrate cell,e.g., an insect cell. In a specific embodiment, the host cell is an SF9cell.

Formulations

Compositions for use in treatment of bleeding disorders are providedherein. Such compositions contain a therapeutically effective amount ofa codon-altered Factor IX polynucleotide, e.g., an AAV gene therapyvector including a codon-altered polynucleotide encoding for Factor IX,as described herein. Therapeutically effective amounts of thecodon-altered FIX polynucleotide (e.g., an AAV gene therapy vectorincluding the codon-altered Factor IX coding sequence) are mixed with asuitable pharmaceutical carrier or vehicle for systemic, topical orlocal administration. Final formulation of the codon-altered Factor IXpolynucleotides disclosed herein will be within the abilities of thoseskilled in the art.

Dosages

The nucleic acid compositions of the invention are administered topatients in need thereof. The amount or dose of the therapeutic genetherapy agent administered depends on factors such as the particularcodon-altered FIX polynucleotide construct, the delivery vector used,the severity of the disease, and the general characteristics of thesubject. The exact dose will depend on the purpose of the treatment, andwill be ascertainable by one skilled in the art using known techniques(see, e.g., Lieberman, Pharmaceutical Dosage Forms (vols. 1-3, 1992);Lloyd, The Art, Science and Technology of Pharmaceutical Compounding(1999); Pickar, Dosage Calculations (1999); and Remington: The Scienceand Practice of Pharmacy, 20th Edition, 2003, Gennaro, Ed., Lippincott,Williams & Wilkins). It is within the abilities of the skilled physicianto determine a particular dosage and dosing regimen for treatment of aparticular subject.

In some embodiments, a gene therapy vector (e.g., an AAV gene therapyvector particle) having a codon-altered Factor IX polynucleotide isadministered intravenously at a therapeutically effective dose to asubject in need thereof (e.g., a subject with mild, moderate, or severehemophilia B). In some embodiments, a therapeutically effective dose isbetween about 2×10E11 and 2×10E14 vector genomes per kilogram bodyweight of the subject. In a specific embodiment, a therapeuticallyeffective dose is between about 2×10E12 and 2×10E13 vector genomes perkilogram body weight of the subject. In some embodiments, the subject isadministered about 2×10E11, 3×10E11, 4×10E11, 5×10E11, 6×10E11, 7×10E11,8×10E11, 9×10E11, 1×10E12, 2×10E12, 3×10E12, 4×10E12, 5×10E12, 6×10E12,7×10E12, 8×10E12, 9×10E12, 1×10E13, 2×10E13, 3×10E13, 4×10E13, 5×10E13,6×10E13, 7×10E13, 8×10E13, 9×10E13, 1×10E14, or 2×10E14 vector genomesper kilogram body weight of the subject.

Accordingly, the disclosure provides methods for treating a Factor IXdeficiency (e.g., hemophilia B). In some embodiments, the methodsinclude administering to a patient in need thereof a codon-alteredFactor IX polynucleotide construct having high nucleotide sequenceidentity (e.g., at least 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100%)to one of a CS02, CS03, CS04, CS05, or CS06 sequence, as describedherein. In some embodiments, the codon-altered Factor polynucleotide hashigh sequence identity to a codon-altered Factor IX pre-pro-polypeptidecoding sequence, e.g., high sequence identity to one of CS02-FL-NA (SEQID NO:5), CS03-FL-NA (SEQ ID NO:6), CS04-FL-NA (SEQ ID NO:7), CS05-FL-NA(SEQ ID NO:8), or CS06-FL-NA (SEQ ID NO:9). In some embodiments, thecodon-altered Factor polynucleotide has high sequence identity to acodon-altered mature Factor IX single-chain polypeptide coding sequence,e.g., high sequence identity to one of CS02-MP-NA (SEQ ID NO: 13),CS03-MP-NA (SEQ ID NO: 14), CS04-MP-NA (SEQ ID NO: 15), CS05-MP-NA (SEQID NO: 16), or CS06-MP-NA (SEQ ID NO:17).

In some embodiments, treatment includes administering to a patient inneed thereof a gene therapy vector including a codon-altered Factor IXpolynucleotide construct having high nucleotide sequence identity (e.g.,at least 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or 100%) to one of aCS02, CS03, CS04, CS05, or CS06 sequence, as described herein. In oneembodiment, the gene therapy vector is a mammalian gene therapy vector.In a specific embodiment, the mammalian gene therapy vector is a viralvector, e.g., a lentivirus, retrovirus, adeno virus, or adeno-associatedvirus vector.

In one embodiment, the gene therapy vector is an adeno-associated virus(AAV) particle harboring a viral vector encoding the codon-alteredFactor IX coding sequence. Generally, the viral vector includes invertedterminal repeats (ITR) at each termini, one or more expressionregulatory elements, a codon-altered Factor IX coding sequence, and apoly-A signal sequence. In a specific embodiment, the gene therapyvector includes a liver-specific regulatory control element (e.g., oneor more copies of a CRM8 element).

Production

The codon-altered Factor IX polynucleotides and viral vectors describedherein (e.g., the nucleic acid compositions) are produced according toconventional methods for nucleic acid amplification and vectorproduction. Two predominant platforms have developed for large-scaleproduction of recombinant AAV vectors. The first platform is based onreplication in mammalian cells, while the second is based on replicationin invertebrate cells. For review, see, Kotin R. M., Hum. Mol. Genet.,20(R1):R2-6 (2011), the content of which is expressly incorporatedherein by reference, in its entirety, for all purposes.

Accordingly, the disclosure provides methods for producing anadeno-associated virus (AAV) particle. In some embodiments, the methodsinclude introducing a codon-altered Factor IX polynucleotide constructhaving high nucleotide sequence identity (e.g., at least 95%, 96%, 97%,98%, 99%, 99.5%, 99.9%, or 100%) to one of a CS02, CS03, CS04, CS05, orCS06 sequence, as described herein, into a host cell where thepolynucleotide construct is competent for replication in the host cell.

In some embodiments, the host cell is a mammalian host cell e.g., anHEK, CHO, or BHK cell. In a specific embodiment, the host cell is an HEK293 cell. In some embodiments, the host cell is an invertebrate cell,e.g., an insect cell. In a specific embodiment, the host cell is an SF9cell.

Treatment

In some embodiments, the nucleic acid compositions (e.g., codon-alteredpolynucleotides) described herein are administered to a subject in needthereof, in accordance with known administrative methods. Methods foradministering gene therapy vectors are well known in the art. Theseinclude, without limitation, intravenous administration, intramuscularinjection, interstitial injection, and intra-hepatic administration(e.g., intra-hepatic artery or vein). For example, see Chuah M K et al.,Hum Gene Ther., 23(6):557-65 (2012); Chuah M K et al., J ThrombHaemost., 10(8): 1566-69 (2012); Chuah M K et al., J Thromb Haemost. 11Suppl 1:99-110 (2013); VandenDriessche et al., Hum Gene Ther. 23(1):4-6(2012); High K A, Blood, 120(23):4482-87 (2012); Matrai et al., MolTher., 18(3):477-90 (2010); and Matrai et al., Curr Opin Hematol.,17(5):387-92 (2010), each of which is hereby incorporated by referenceherein, for review.

Assessing Therapeutic Efficacy

The therapeutic efficacy of a hemophilia B treatment can be evaluated,for example, by measuring the Factor IX-dependent coagulation potentialof blood from a subject being treated. Metrics for assessing coagulationpotential include, without limitation, in vitro activated partialthromboplastin time assay (APPT), Factor IX chromogenic activity assays,blood clotting times, and Factor IX antigen levels (e.g., using a FactorIX-specific ELISA). It should be noted that a therapeutic dose need notresult in wild-type levels of FIX in a patient; rather, sufficientexpression to decrease symptoms in a meaningful or measurable way isconsidered therapeutic for the purposes of the invention.

According to the National Hemophilia Foundation, a subject is classifiedas having mild hemophilia B when their blood plasma contains between 6%and 49% of the Factor IX activity of normal human blood plasma. Subjectswith mild hemophilia B typically experience bleeding only after seriousinjury, trauma or surgery. In many cases, mild hemophilia is notdiagnosed until an injury, surgery or tooth extraction results inprolonged bleeding. The first episode may not occur until adulthood.Women with mild hemophilia often experience menorrhagia, heavy menstrualperiods, and can hemorrhage after childbirth.

According to the National Hemophilia Foundation, a subject is classifiedas having moderate hemophilia B when their blood plasma contains between1% and 5% of the Factor IX activity of normal human blood plasma.Subjects with moderate hemophilia B tend to have bleeding episodes afterinjuries. Bleeds that occur without obvious cause are called spontaneousbleeding episodes.

According to the National Hemophilia Foundation, a subject is classifiedas having severe hemophilia B when their blood plasma contains less than1% of the Factor IX activity of normal human blood plasma. Subjects withsevere hemophilia B experience bleeding following an injury and may havefrequent spontaneous bleeding episodes, often into their joints andmuscles.

In some embodiments, normal human blood plasma is defined as containing1 IU of Factor IX activity per mL. Thus, in some embodiments, bloodplasma from a subject classified with mild hemophilia B contains between0.06 and 0.49 IU of Factor IX activity per mL. In some embodiments,blood plasma from a subject classified with moderate hemophilia Bcontains between 0.01 and 0.05 IU of Factor IX activity per mL. In someembodiments, blood plasma from a subject classified with severehemophilia B contains between 0.01 and 0.05 IU of Factor IX activity permL.

Accordingly, in some embodiments, hemophilia B therapy istherapeutically effective when it raises the average level of Factor IXactivity in the subject's blood/plasma. In some embodiments, atherapeutically affective treatment raises the average level of FactorIX activity in the subject's blood/plasma by at least 1%, 2%, 3%, 4%,5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, ormore. In a specific embodiment, a therapeutically effective hemophiliatherapy increases the average Factor IX activity in the blood/plasma ofa subject by at least 5%. In another specific embodiment, atherapeutically effective hemophilia therapy increases the averageFactor IX activity in the blood/plasma of a subject by at least 10%. Inanother specific embodiment, a therapeutically effective hemophiliatherapy increases the average Factor IX activity in the blood/plasma ofa subject by at least 15%. In another specific embodiment, atherapeutically effective hemophilia therapy increases the averageFactor IX activity in the blood/plasma of a subject by at least 20%. Inanother specific embodiment, a therapeutically effective hemophiliatherapy increases the average Factor IX activity in the blood/plasma ofa subject by at least 25%. In another specific embodiment, atherapeutically effective hemophilia therapy increases the averageFactor IX activity in the blood/plasma of a subject by at least 30%.

In some embodiments, a therapeutically effective treatment raises theaverage level of Factor IX activity in the subjects blood such that thesubject is classified as having a less severe form of hemophilia B. Forexample, in one embodiment, a subject originally classified with severehemophilia B is reclassified with moderate hemophilia B or mildhemophilia B after undergoing a therapeutically effective treatment. Inanother embodiment, a subject originally classified with moderatehemophilia B is reclassified with mild hemophilia B after undergoing atherapeutically effective treatment.

VI. Examples Example 1—Codon-Altered Factor IX Expression SequencesEnhance FIX Expression Levels

In order to generate gene therapy constructs providing improvedexpression of heterologous Factor IX in vivo, a panel ofself-complementary AAV8-based vectors encoding a full-length Factor IXpreproprotein with an R384L amino acid substitution (FIXp-FL-AA SEQ IDNO:4)) were constructed. The Factor IX coding sequence of each constructwas altered to improve expression in humans through several steps. EachFactor IX coding sequence was modified according to an algorithmdesigned to account for preferred/disfavored sequence motifs and to skewcodon-usage towards preferred human codons. Several algorithms were usedfor this first step, as reported in Table 2. Intermediate codon-alteredsequences, resulting from application of the algorithms reported inTable 2, where then further modified manually to reduce or eliminate CpGdinucleotides, adjust the final GC content, adjust to allow forpreferred codon pairs, adjust to avoid disfavored codon pairs, andadjust the final codon usage. For further information on theseconsiderations, see, e.g., Fath S. et al., PLoS. One., 6, e17596 (2011);Haas J. et al., Curr. Biol., 6, 315-324 (1996); Tats A., BMC Genomics.9:463 (2008), Grote A. et al., Nucleic Acids Research, 33(Web Serverissue), W526-W531 (2005), Mirsafian H. et al., Scientific WorldJournal., 639682 (2014), and Pechmann S. et al., Nat Struct Mol Biol.20(2):237-43 (2013), the contents of which are expressly incorporatedhereinby reference, in their entireties, for all purposes, specificallyfor their teachings of codon alteration considerations.

Each generated codon-altered coding sequence (e.g., CS02, CS03, CS04,CS05, and CS06, shown in FIGS. 5 through 9, respectively) encoded for anidentical FIX(R384L) protein (FIXp-FL-AA (SEQ ID NO:4)). The CS02, CS03,and CS04 constructs contain no CpG motifs, while CS05 and CS06 contain11 and 3 CpGs, respectively.

To use as controls, vector constructs incorporating wild-type FIX codingsequences, with and without R384L Padua amino acid substitutions, werealso generated. The WH01 construct encodes a wild type FIX preproproteinwithout the R384L Padua mutation, and includes 20 CpG dinucleotides. TheWH02 construct encodes a wild type FIX preproprotein with the R384LPadua mutation, and includes 19 CpG dinucleotides.

The WH01 and WH02 constructs include 20 and 19 CpGs in their codingsequences, respectively. In contrast, the CS02, CS03, and CS04constructs contain no CpG motifs, while the CS05 and CS06 constructscontain 11 and 3 CpGs, respectively.

As shown in FIG. 1A, the codon-altered Factor IX coding sequences wereinserted into an Adeno-associated virus (“AAV”) transgene cassettecontaining a mouse transthyrethrin enhancer/promoter (SEQ ID NO:52), amouse minute virus (“MVM”) intron (SEQ ID NO:53), the codon-altered FIXconstruct including the R384L “Padua” amino acid substitution (U.S. Pat.No. 6,531,298; Simione et al., NEJM 361:1671-75 (2009); the R384Lmutation is commonly reported as an R338L mutation, referring to theposition of the wild-type arginine in the human single-chain FIX proteinlacking the signal and propeptide), followed by a bovine growth hormonepolyA element (SEQ ID NO:54). The gene cassette is flanked by AAV2inverted terminal repeats (“ITR”) (SEQ ID NOs:51 and 55). The left ITRrepeat includes a mutation in the terminal concatemer resolution siteresulting in the self-complementary (sc) phenotype of the vectors. Thebasic vector design is described in detail in Wu et al., Mol. Ther.16:280-89 (2008) and in PCT Publication Number WO 2014/064277 A1, thecontents of which are incorporated herein by reference, in theirentireties, for all purposes.

The CS and WH Factor IX AAV constructs were administered toB6/129P2-F9tm1Dws FIX knockout mice (described in Lin et al., Blood,90:3962-66 (1997), the content of which is incorporated by referenceherein, in its entirety, for all purposes). AAV vector dilutions wereinjected into animals (4-8 animals per group) via the lateral tail veinbased upon the individual animals body weights (4×10E11 vectorgenomes/kilogram (vg/kg) body weight). Blood samples were collected atdefined time intervals by retro-orbital puncture after dosing accordingto known procedures using glass capillaries. Blood was then transferredto a tube pre-filled with sodium citrate anticoagulant and plasma wasobtained by standard procedures and frozen at −20° C.

Expression of the various Factor IX constructs was determined and plasmaFIX levels at day 14 in FIX knockout mice were used to judge the potencyof the constructs after tail vein injection of the vectors into themice, as reported in Table 2. By day 14, expression levels in theknockout mouse model have nearly reached the maximum FIX expression. Asshown in Table 2, the WH02 FIX(R384L) control construct was expressed at1.03 units FIX at day 14 after administration of 4×10E11 vectorgenomes/kilogram (vg/kg) body weight. This expression level was used asa baseline to determine fold-enrichment of the codon-altered Factor IXconstructs. As reported in Table 2, the CS codon-altered constructsprovided between about 2-fold and 4-fold increased expression, ascompared to the WH02 control construct, encoded by a wild-typepolynucleotide sequence. Most notably, the CS06 codon-altered constructprovided 4.2-fold greater Factor IX activity than the WH002 controlconstruct and 21.6-fold greater Factor IX activity than the WH01(wild-type Factor IX) control construct.

TABLE 2 Expression of Factor IX from contracts with wild-type codonsequences (WH01 - wtFIX; WH02 - FIX(R384L) and codon-altered sequences(CS02-CS06). Fold Fold Day 14 expression expression AAV Numberexpression levels compared compared Construct Modification of vectorgenome of CpGs [% hum FIX] to WH01 to WH02 WH01 Human FIX wild-typesequence 20 0.20 1.0 0.19 (GeneBank NM000133.3) without R338L (Padua)mutation WH02 Human FIX wild-type sequence 19 1.03 5.2 1.0 with R338L(Padua) mutation CS02 Human FIX sequence with R338L 0 2.12 10.6 2.1mutation; Geneart basic algorithm further optimized towards human serumalbumin codons. CS03 Human FIX sequence with R338L 0 1.98 9.9 1.9mutation; Geneart basic algorithm further optimized towards mostfrequently used human codons (Haas et al., 1996. Curr Biol. 6, 315-324). CS04 Human FIX sequence with R338L 0 2.77 13.9 2.7 mutation;Geneart basic algorithm further optimized towards liver codon usage asdescribed in Uhlen et al., 2015 Science 347, 6220. CS05 Human FIXsequence with R338L 11 3.93 19.7 3.8 mutation; JCAT algorithm modifiedto reduce CpGs; (Grote et al., 2005. Nucleic Acids Res 1, 33). CS06Human FIX sequence with R338L 3 4.32 21.6 4.2 mutation; Geneart basicalgorithm further optimized towards most frequently used human codons(Haas et al., 1996. Curr Biol. 6, 315- 324).

Example 2—Liver-Specific CRM8 Elements Enhance Expression of FIX in Mice

To further increase Factor IX expression and activity from thecodon-altered constructs, one to three copies of a liver-specificcis-regulatory control element (CRM8 (SEQ ID NO:39)), as reported inNair et al., Blood 123:3195-99 (2014) was incorporated into the genecassette, creating the construct diagramed in FIG. 1B. AAV vectorsharboring the CS02 codon-altered FIX coding sequence with zero(CS02-CRM8.0-V), one (CS02-CRM8.1-V), two (CS02-CRM8.2-V), or three(CS02-CRM8.3-V) CRM8 control elements were injected into wild-type miceby the tail vein route. Human FIX antigen in mouse plasma was thenmeasured over time with a human FIX-specific ELISA assay.

As reported in Table 3, use of CRM8 regulatory elements increased FactorIX expression in vivo by about 2-fold and 4-fold, as compared toexpression from the control construct lacking a CRM8 element, 21-dayspost infection. For example, the CS02-CRM8.1-V vector, containing asingle CRM8 element, provided twice the expression of FIX as did theCS02-CRM8.0-V control vector. The inclusion of multiple copies of theCRM8 element further improved this expression. For example, vectorscontaining 2 copies of the CRM8 element provided three-fold expressionand vectors containing 3 copies of the CRM8 element provided 3.4-foldexpression, relative to the control vector.

TABLE 3 Factor IX expression levels in the plasma of wild- type miceinjected with codon-altered AAV vectors with 0-3 copies of a CRM8regulatory control element. # of FIX FIX FIX Fold AAV CRM8 (ng/ml)(ng/ml) (ng/ml) increase # construct elements Day 4 Day 11 Day 21 Day 211 CS02-CRM8.0- 0 65.8 133.4 239.2 1.0 scV 2 CS02-CRM8.1- 1 120.7 250.7442.8 1.9 scV 3 CS02-CRM8.2- 2 152.9 417.3 713.8 3.0 scV 4 CS02-CRM8.3-3 130.9 432.6 800.9 3.4 scV

Example 3—Liver-Specific CRM8 Elements Enhance Expression of FIX inHuman Hepatic Cells

The CS02 Factor IX gene therapy constructs containing 0-3 copies of theCRM8 liver-specific regulatory control element, as described in Example2, were further tested by in vitro biopotency assays performed with thehuman hepatic cell line HepG2. Briefly, HepG2 cells were infected withone of the CS02-CRM8-V AAV vectors, as described in Example 2, and FIXactivity was measured by a chromogenic substrate assay three days afterinfection. Consistent with the results reported in Example, 2, allvectors containing a CRM8 regulatory control element provided higher FIXexpression, as reported in Table 4. Striking, the effect of usingmultiple CRM8 elements was even more pronounced in the human HepG2 cellsthan in the mouse model. For example, vectors containing 2 copies of theCRM8 element provided 6.7-fold expression and vectors containing 3copies of the CRM8 element provided 12.8-fold expression, relative tothe control vector. This confirms the positive effects that the CRM8regulatory control element has on FIX expression in these vectors.

TABLE 4 Factor IX expression levels in human hepatic HepG2 cellsinjected with codon-altered AAV vectors with 0-3 copies of a CRM8regulatory control element. # of CRM8 FIX activity AAV constructelements [Biopotency units] Fold increase CS02-CRM8.0-scV 0 0.35 1CS02-CRM8.1-scV 1 0.82 2.3 CS02-CRM8.2-scV 2 2.36 6.7 CS02-CRM8.3-scV 34.48 12.8

Example 4—Single Stranded FIX AAV8 Vectors Provide Similar In VivoExpression as Comparable Self-Complementary Vectors

In some instances, self-complementary (sc) AAV vectors express atransgene cassette more efficiently than a similar single-stranded (ss)AAV vector. This is presumably due to more rapid double strand formationafter uncoating of a self-complementary vector genome in the cellnucleus. For review, see, McCarty D., Mol. Ther., (16):1648-56 (2008),the content of which is incorporated herein by reference, in itsentirety, for all purposes.

A recent study confirmed this effect using an EGFP vector. Bell et al.,Hum. Gene Ther. Methods, (27):228-37 (2016). However, the study alsoshowed that this effect was transgene and dose dependent. For example, ahuman ornithine transcarbamylase (hOTC) gene cassette in aself-complementary AAV8 vector showed better expression at low dose inthe liver of mice as compared to a corresponding single-stranded vector.However, this effect could not be demonstrated at a high dose suggestingthat the effect, at least in the non-secreted gene studied, wastransgene and dose dependent. Id.

In order to explore the properties of the disclosed codon-altered FIXgene constructs in the context of single-stranded and self-complementarydesign, single-stranded constructs harboring a CS06 codon-alteredFIX(R338L) gene and two intact ITRs were constructed with and withoutCRM8 regulatory control elements, as diagramed in FIGS. 1D and 1C,respectively. The single-stranded (ss) vectors were produced in anHEK293 cell system, and Factor IX expression was compared to expressionof the self-complementary constructs reported in Examples 1-3.

First, the self-complementary (sc) and single-stranded (ss)CS06-CRM8.0-V constructs were tested in vivo following injection intoB6/129P2-F9tm1Dws FIX knockout mice, as described above. Surprisingly,as reported in Table 5, the self-complementary (sc) and single-stranded(ss) CS06 vector constructs showed very similar plasma levels of FIXactivity, suggesting the reported advantage of sc vectors, as comparedto ss vectors, does not hold for the codon-altered Factor IX constructsdescribed herein. Expression is dependent on many parameters includingthe transgene construct, the stability of transcript, the promoter(s)used in the construct, time, and dose. As shown in Table 5, under theconditions chosen to correct bleeding and obtain long-term expression inFIX ko mice, the corresponding sc and ss vectors provided substantiallysimilar expression levels.

The effects of the liver-specific CRM8 regulatory control element on FIXexpression was also investigated in the single-stranded vectorbackground. As reported in Table 5, inclusion of one CRM8 element in thesingle-stranded vector improved FIX expression in the B6/129P2-F9tm1DwsFIX knockout mice. Inclusion of three CRM8 elements further improved FIXexpression from the single-stranded CS06 construct, to levels slightlymore than 2-fold above the self-complementary CS06 control, lacking aCRM8 element. As compared to the wild-type WH02 construct, thesingle-stranded CS06 vectors provided up to 7-fold greater expression,when paired with three CRM8 regulatory control elements.

TABLE 5 Factor IX expression levels in FIX knockout mice injected withvarious single-stranded (ss) and self-complementary (sc) AAV Factor IXvectors. Fold Fold increase increase # of Expr Expr Expr vs CS06 vs WH02AAV CRM8 level¹ level level (d 7/d (d 7/d construct elements (d 7) (d14) (d 28) 14/d 28) 14/d 28) CS06- 0 1.38 2.73 2.99 0.7/0.9/0.91.5/2.7/2.7 CRM8.0- ssV CS06- 1 1.92 3.57 3.47 1.0/1.1/1.0 2.1/3.5/3.2CRM8.1- ssV CS06- 3 4.43 6.65 7.78 2.3/2.1/2.2 4.9/6.5/7.1 CRM8.3- ssV(SEQ ID NO: 40) CS06- 0 1.89 3.17 3.50 1.0/1.0/1.0 2.1/3.1/3.2 CRM8.0-scV WH02- 0 0.90 1.03 1.10 0.5/0.3/0.3 1.0 CRM8.0- scV ¹FIX activity inInternational Units (average of 7-8 mice); d, day;

Example 5—Single Stranded FIX AA V8 Vectors Provide Better FIXExpression in Human Hepatic Cells than Comparable Self-ComplementaryVectors

Factor IX expression from the single-stranded CS06 vectors described inExample 4 was then investigated in human HepG2 cells and compared tosimilar self-complementary vector constructs. Consistent with the invivo results reported in Example 4, single-stranded CS06 vectors withouta CRM8 element provided FIX expression at slightly lower levels than acomparative self-complementary vector in HepG2 cells. However, inclusionof a single CRM8 element increased FIX expression from thesingle-stranded CS06 vector to a level 2.6-times greater than expressionfrom the self-complementary CS06 vector, as reported in Table 6.

Most surprisingly, however, inclusion of three CRM8 elements in thesingle-stranded CS06 vector increased FIX expression to a level16.8-times greater than expression from the self-complementary CS06vector. The increased FIX expression was more than 100-times greaterthan FIX expression from the WH02 control vector. In summary, thesingle-stranded CS06 vector containing three CRM8 elements provides thehighest expression levels in both the in-vivo and the in-vitrobiopotency assays.

TABLE 6 Factor IX expression levels from single-stranded (ss) andself-complementary vectors in human hepatic cells. # of FIX activityCRM8 [Biopotency Fold increase vs Fold increase vs AAV constructelements units] CS06-CRM8.0-scV WH02-CRM8.0-scV CS06-CRM8.0-ssV 0 0.240.6 3.9 CS06-CRM8.1-ssV 1 0.95 2.6 15.9 CS06-CRM8.3-ssV 3 6.20 16.8103.3 (SEQ ID NO: 40) CS06-CRM8.0-scV 0 0.37 1.0 6.2 WH02-CRM8.0-scV 00.06 0.2 1.0

Materials and Methods for Examples 1-5

Animal Experiments.

For the experiments in FIX knockout model, the FIX ko mouse strainB6/129P2-F9tm1Dws (developed by Lin et al., 1997. Blood 90:3962-6) wereused. In the wild-type mouse model 4-5 week old male C57BL6-J B16 micewere used. Both strains were obtained from commercial breeders. The AAVvector dilutions were injected into animals (4-8 animals per group) viathe lateral tail vein based upon the individual animals body weights.Blood sampling was done at defined time intervals by retro-orbitalpuncture after dosing according to known procedures using glasscapillaries. Blood was then transferred to a tube pre-filled with sodiumcitrate anticoagulant and plasma was obtained by standard procedures andfrozen at −20° C.

In Vitro Biopotency Assay in HepG2 Cells Including FIX ChromogenicSubstrate Assay.

The in vitro biopotency assay for gene therapy vector preparations wasperformed in the human hepatic cell line HepG2 (ATCC HB-8065). Aftertreatment with hydroxyurea, cells were infected with AAV8FIX vectors andincubated for approximately 96 hrs. During incubation time, FIX wasexpressed and released into the cell supernatant and FIX-activity wasdetermined by chromogenic endpoint measurement (Rossix AB, Sweden). Eachassay run includes a standard curve of purified AAV-FIX vector materialusing MOI ranging between 700 and 7000. FIX activity of the standard atMOI 3270 is set as Bio Potency Unit (BPU) of 1.

Human FIX Quantifications in Mouse Plasma.

To quantify human FIX in knock-out mouse plasma FIX coagulation assayswere performed using standard FIX coagulation analytics. To quantifyhuman FIX antigen in plasma of the wild-type mice a commerciallyavailable ELISA kit (ASSERACHROM IX:AG (cat. nr. 00943 Stago BNL) wasused that specifically detects human FIX.

Example 6—Improved Transcriptional Efficacy by Incorporation of CRM8Elements

To address whether improved biopotency of CRM8-containing vectorsresults from increased transcriptional efficacy, a human liver cell line(HepG2) and mouse liver cells (FIX knock-out mice) were transduced withsingle-stranded CS06 vectors containing 0, 1, or 3 CRM8 elements. FIXmRNA and DNA levels were determined and presented as ratio betweennormalized FIX mRNA and DNA levels.

In the in vitro model, inclusion of one CRM8 element (CS06-CRM8.1-ssV)or three CRM8 elements (CS06-CRM8.3-ssV (SEQ ID NO:40)) resulted in5-fold and 23-fold higher human FIX mRNA levels in transduced humanhepatic cells than in cells transduced with vector lacking a CRM8element (CS06-CRM8.0-ssV) (Table 6), respectively. Similarly, in the invivo model, FIX expression in murine liver from vectors containing oneor three CRM8 elements was 2.0-fold and 2.8-fold higher than FIXexpression from vector lacking a CRM8 element (Table 6), respectively.Both models support that CRM8 element(s) provide a beneficial effect inimproving transcriptional activity of a FIX construct.

TABLE 7 FIX mRNA levels following AAV8-FIX transduction of a human livercell line or mouse liver. In vitro hepatic cell line (HepG2) In vivomouse liver tissue Normalized FIX Fold increase vs Normalized FIX Foldincrease vs AAV construct ratio: mRNA/DNA CS06-CRM8.0-ssV ratio:mRNA/DNA CS06-CRM8.0-ssV CS06-CRM8.0-ssV 0.025 1 0.38 1 CS06-CRM8.1-ssV0.14 5.4 0.78 2.0 CS06-CRM8.3-ssV 0.58 23.4 1.09 2.8

Methods for Example 6

Quantitative real-time polymerase chain reaction including RNA and DNAextraction. Genomic DNA and total RNA were extracted from frozen livers(see animal experiments) or HepG2 cells (see in vitro biopotency assayin HepG2 cells) by standard procedures. For analytics of the in vivoexperiments, a subset of three animals per treatment group close to themean FIX activity of the respective group at day 14 (inside the mean±SD)was selected. cDNA was synthesized using an oligo (dT20) primer, theSuperScript III reverse transcriptase (RT) and DNase-treated total RNAaccording to the manual (DNeasy Blood & Tissue Kit, Qiagen, Germany;RNeasy mini kit, Qiagen).

FIX-transgene copy numbers in both gDNA and cDNA samples were determinedby a fluorescent-based quantitative real-time polymerase chain reaction(qPCR), amplifying a 96 bp sequence of FIX exon 6. Murine β-actin servedas endogenous control and was quantified using a commercially availableTaqMan assay. qPCR data analysis was performed using the specificdevice's software, calculating the FIX or β-actin copies per reactionbased on the linear regression parameters of the standard curve.Further, the results were normalized to 1 μg of either RNA or DNA andthe mRNA:DNA ratio was calculated.

It is understood that the examples and embodiments described herein arefor illustrative purposes only and that various modifications or changesin light thereof will be suggested to persons skilled in the art and areto be included within the spirit and purview of this application andscope of the appended claims. All publications, patents, and patentapplications cited herein are hereby incorporated by reference in theirentirety for all purposes.

1. A nucleic acid composition, comprising a Factor IX polynucleotideencoding a Factor IX protein, said Factor IX polynucleotide comprising anucleic acid sequence that is least 97% identical to the nucleic acidsequence of CS06-MP-NA (SEQ ID NO:17).
 2. The nucleic acid compositionof claim 1, wherein the Factor IX polynucleotide comprises a nucleicacid sequence that is at least 99% identical to the nucleic acidsequence of CS06-MP-NA (SEQ ID NO:17).
 3. The nucleic acid compositionof claim 1, wherein the Factor IX polynucleotide has no more than 10 CpGdinucleotides.
 4. The nucleic acid composition of claim 1, wherein theFactor IX polynucleotide has no more than 3 CpG dinucleotides.
 5. Thenucleic acid composition of claim 1, wherein the Factor IXpolynucleotide comprises the nucleic acid sequence of CS06-MP-NA (SEQ IDNO: 17).
 6. The nucleic acid composition of claim 1, wherein the FactorIX polynucleotide encodes for leucine at nucleotide positions 1150-1152,relative to FIX-FL-NA (SEQ ID NO:1).
 7. The nucleic acid composition ofclaim 1, wherein the Factor IX protein encoded by the Factor IXpolynucleotide has from 1 to 10 amino acid substitutions as compared toFIXp-MP-AA (SEQ ID NO: 12).
 8. The nucleic acid composition of claim 1,wherein the Factor IX protein encoded by the Factor IX polynucleotidehas the amino acid sequence of FIXp-MP-AA (SEQ ID NO: 12).
 9. Thenucleic acid composition of claim 1, wherein the Factor IXpolynucleotide further comprises a pre-pro-leader polynucleotideencoding a pre-pro-leader peptide, said pre-pro-leader peptidecomprising the amino acid sequence of FIX-PPP-AA (SEQ ID NO:36).
 10. Thenucleic acid composition of claim 9, wherein the pre-pro-leaderpolynucleotide has the nucleic acid sequence of CS06-PPP-NA (SEQ IDNO:23).
 11. The nucleic acid composition of claim 1, wherein the FactorIX polynucleotide has a nucleic acid sequence that is at least 99%identical to the nucleic acid sequence of CS06-FL-NA (SEQ ID NO:9). 12.The nucleic acid composition of claim 1, wherein the Factor IXpolynucleotide has the nucleic acid sequence of CS06-FL-NA (SEQ IDNO:9).
 13. A nucleic acid composition, comprising a Factor IXpolynucleotide encoding a Factor IX protein, said Factor IXpolynucleotide comprising a nucleic acid sequence that is least 95%identical to the nucleic acid sequence of CS02-MP-NA (SEQ ID NO: 13).14. A nucleic acid composition, comprising a Factor IX polynucleotideencoding a Factor IX protein, said Factor IX polynucleotide comprising anucleic acid sequence that is least 98% identical to the nucleic acidsequence of CS03-MP-NA (SEQ ID NO: 14).
 15. A nucleic acid composition,comprising a Factor IX polynucleotide encoding a Factor IX protein, saidFactor IX polynucleotide comprising a nucleic acid sequence that isleast 99% identical to the nucleic acid sequence of CS04-MP-NA (SEQ IDNO:15).
 16. A nucleic acid composition, comprising a Factor IXpolynucleotide encoding a Factor IX protein, said Factor IXpolynucleotide comprising a nucleic acid sequence that is least 98%identical to the nucleic acid sequence of CS05-MP-NA (SEQ ID NO:16).17-22. (canceled)
 23. The nucleic acid composition of claim 1, furthercomprising a liver-specific promoter element operably linked to theFactor IX polynucleotide.
 24. The nucleic acid composition of claim 23,wherein the liver-specific promoter element comprises one copy of apromoter polynucleotide, said promoter polynucleotide comprising anucleic acid sequence that is least 95% identical to CRM8 (SEQ IDNO:39).
 25. The nucleic acid composition of claim 23, wherein theliver-specific promoter element comprises three copies of a promoterpolynucleotide, said promoter polynucleotide comprising a nucleic acidsequence that is least 95% identical to CRM8 (SEQ ID NO:39).
 26. Thenucleic acid composition of claim 25, wherein said promoterpolynucleotide comprises the nucleic acid sequence of CRM8 (SEQ IDNO:39).
 27. The nucleic acid composition of claim 1, further comprisingan intron operatively linked to the Factor IX polynucleotide.
 28. Thenucleic acid composition of claim 27, wherein the intron comprises anMVM intron polynucleotide comprising a nucleic acid sequence that is atleast 95% identical to MVMI (SEQ ID NO:53).
 29. The nucleic acidcomposition of claim 28, wherein said MVM intron polynucleotidecomprises the nucleic acid sequence of MVMI (SEQ ID NO:53).
 30. Thenucleic acid composition of claim 29, wherein said intron is positionedbetween a promoter element and the translation initiation site of thenucleotide sequence encoding a Factor IX polypeptide.
 31. The nucleicacid composition of claim 1, comprising the nucleic acid sequence ofCS06-CRM8.3-ssV (SEQ ID NO:40).
 32. The nucleic acid composition ofclaim 1, comprising a mammalian gene therapy vector.
 33. The nucleicacid composition of claim 32, wherein the mammalian gene therapy vectoris an adeno-associated virus (AAV) vector.
 34. The nucleic acidcomposition of claim 33, wherein said adeno-associated virus vector is aserotype 8 adeno-associated virus (AAV-8) vector.
 35. The nucleic acidcomposition of claim 33, wherein the mammalian gene therapy vectorcomprises a single-stranded polynucleotide encoding the Factor IXprotein.
 36. A method for treating hemophilia B comprising administeringto a patient in need thereof a nucleic acid composition according toclaim
 1. 37-38. (canceled)
 39. A method for producing anadeno-associated virus (AAV) particle comprising introducing a nucleicacid composition according to claim 1 into a mammalian host cell,wherein the nucleic acid composition is competent for replication in themammalian host cell.